diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..a43c180d --- /dev/null +++ b/Makefile @@ -0,0 +1,92 @@ +SRC_DIR = src +SCHEMA_DIR = $(SRC_DIR)/schema +SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml') +SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES)) + +TARGETDIR = . + +SCHEMA_NAME = mixs +SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml +TGTS = graphql jsonschema docs shex owl csv graphql python + +#GEN_OPTS = --no-mergeimports +GEN_OPTS = + +all: gen-all +gen: $(patsubst %,gen-%,$(TGTS)) + +t: + echo $(SCHEMA_NAMES) + +echo: + echo $(patsubst %,gen-%,$(TGTS)) + +test: all + +install: + . environment.sh + pip install -r requirements.txt + +tdir-%: + mkdir -p $(TARGETDIR)/$* +docs: + mkdir $@ + +stage: $(patsubst %,stage-%,$(TGTS)) +stage-%: gen-% + cp -pr $(TARGETDIR)/$* . + + +### -- MARKDOWN DOCS -- +# Generate documentation ready for mkdocs +# TODO: modularize imports +gen-docs: $(TARGETDIR)/mixs6/index.md +.PHONY: gen-docs +$(TARGETDIR)/mixs6/%.md: $(SCHEMA_SRC) + gen-markdown $(GEN_OPTS) --dir $(TARGETDIR)/mixs6 $< + +### -- MARKDOWN DOCS -- +# TODO: modularize imports. For now imports are merged. +gen-graphql:$(TARGETDIR)/graphql/$(SCHEMA_NAME).graphql +$(TARGETDIR)/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql + gen-graphql $(GEN_OPTS) $< > $@ + +### -- JSON schema -- +# TODO: modularize imports. For now imports are merged. +gen-jsonschema: $(TARGETDIR)/jsonschema/$(SCHEMA_NAME).schema.json +$(TARGETDIR)/jsonschema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-jsonschema + gen-json-schema $(GEN_OPTS) -t transaction $< > $@ + +### -- Shex -- +# one file per module +gen-shex: $(patsubst %, $(TARGETDIR)/shex/%.shex, $(SCHEMA_NAMES)) +$(TARGETDIR)/shex/%.shex: $(SCHEMA_DIR)/%.yaml tdir-shex + gen-shex --no-mergeimports $(GEN_OPTS) $< > $@ + +### -- CSV -- +# one file per module +gen-csv: $(patsubst %, $(TARGETDIR)/csv/%.csv, $(SCHEMA_NAMES)) +$(TARGETDIR)/csv/%.csv: $(SCHEMA_DIR)/%.yaml tdir-csv + gen-csv $(GEN_OPTS) $< > $@ + +### -- OWL -- +# TODO: modularize imports. For now imports are merged. +gen-owl: $(TARGETDIR)/owl/$(SCHEMA_NAME).owl.ttl +.PHONY: gen-owl +$(TARGETDIR)/owl/%.owl.ttl: $(SCHEMA_DIR)/%.yaml tdir-owl + gen-owl $(GEN_OPTS) $< > $@ + +### -- RDF (direct mapping) -- +# TODO: modularize imports. For now imports are merged. +gen-rdf: $(TARGETDIR)/rdf/$(SCHEMA_NAME).ttl +$(TARGETDIR)/rdf/%.ttl: $(SCHEMA_DIR)/%.yaml tdir-rdf + gen-rdf $(GEN_OPTS) $< > $@ + +### -- LinkML -- +# linkml (copy) +# one file per module +gen-linkml: $(TARGETDIR)/linkml/$(SCHEMA_NAME).yaml +$(TARGETDIR)/linkml/%.yaml: $(SCHEMA_DIR)/%.yaml tdir-limkml + cp $< > $@ + + diff --git a/index.md b/index.md index bbfc7f3e..66136973 100644 --- a/index.md +++ b/index.md @@ -1,7 +1,7 @@ {% include header.html %}
-

THIS IS A DEVELOPMENT VERSION OF THE GSC Website

+

THIS IS A DEVELOPMENT VERSION OF THE GSC Website (cjm version)

For the live website, please visit https://gensc.org/.


diff --git a/mixs6/AddRecovMethodEnum.md b/mixs6/AddRecovMethodEnum.md new file mode 100644 index 00000000..f61f39d8 --- /dev/null +++ b/mixs6/AddRecovMethodEnum.md @@ -0,0 +1,19 @@ + +# Enum: add_recov_method_enum + + + + +URI: [mixs.vocab:add_recov_method_enum](https://w3id.org/mixs/vocab/add_recov_method_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Air.md b/mixs6/Air.md new file mode 100644 index 00000000..60d4738f --- /dev/null +++ b/mixs6/Air.md @@ -0,0 +1,169 @@ + +# Class: Air + + +air + +URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIUVIG],[AirMISAG],[AirMIMARKSSurvey],[AirMIMARKSSpecimen],[AirMIMAG],[AirMIGSVirus],[AirMIGSPlant],[AirMIGSOrg],[AirMIGSEukaryote],[AirMIGSBacteria],[AirME],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMIGSBacteria.md b/mixs6/AirMIGSBacteria.md new file mode 100644 index 00000000..1376f6ab --- /dev/null +++ b/mixs6/AirMIGSBacteria.md @@ -0,0 +1,400 @@ + +# Class: AirMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + +URI: [mixs.vocab:AirMIGSBacteria](https://w3id.org/mixs/vocab/AirMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Air]^-[AirMIGSBacteria],[Air],[MIGSBacteria]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIGSEukaryote.md b/mixs6/AirMIGSEukaryote.md new file mode 100644 index 00000000..9c2969ee --- /dev/null +++ b/mixs6/AirMIGSEukaryote.md @@ -0,0 +1,400 @@ + +# Class: AirMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package air + +URI: [mixs.vocab:AirMIGSEukaryote](https://w3id.org/mixs/vocab/AirMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Air]^-[AirMIGSEukaryote],[Air],[MIGSEukaryote]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIGSPlant.md b/mixs6/AirMIGSPlant.md new file mode 100644 index 00000000..20fdac0d --- /dev/null +++ b/mixs6/AirMIGSPlant.md @@ -0,0 +1,370 @@ + +# Class: AirMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package air + +URI: [mixs.vocab:AirMIGSPlant](https://w3id.org/mixs/vocab/AirMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Air]^-[AirMIGSPlant],[Air],[MIGSPlant]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIGSVirus.md b/mixs6/AirMIGSVirus.md new file mode 100644 index 00000000..0a1015d6 --- /dev/null +++ b/mixs6/AirMIGSVirus.md @@ -0,0 +1,395 @@ + +# Class: AirMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + +URI: [mixs.vocab:AirMIGSVirus](https://w3id.org/mixs/vocab/AirMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Air]^-[AirMIGSVirus],[Air],[MIGSVirus]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/AirMIMARKSSpecimen.md b/mixs6/AirMIMARKSSpecimen.md new file mode 100644 index 00000000..de955396 --- /dev/null +++ b/mixs6/AirMIMARKSSpecimen.md @@ -0,0 +1,320 @@ + +# Class: AirMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package air + +URI: [mixs.vocab:AirMIMARKSSpecimen](https://w3id.org/mixs/vocab/AirMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Air]^-[AirMIMARKSSpecimen],[Air],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIMARKSSurvey.md b/mixs6/AirMIMARKSSurvey.md new file mode 100644 index 00000000..a8a16564 --- /dev/null +++ b/mixs6/AirMIMARKSSurvey.md @@ -0,0 +1,300 @@ + +# Class: AirMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package air + +URI: [mixs.vocab:AirMIMARKSSurvey](https://w3id.org/mixs/vocab/AirMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Air]^-[AirMIMARKSSurvey],[Air],[MIMARKSSurvey]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMe.md b/mixs6/AirMe.md new file mode 100644 index 00000000..5e56040d --- /dev/null +++ b/mixs6/AirMe.md @@ -0,0 +1,335 @@ + +# Class: AirME + + +Combinatorial checklist Metagenome or Environmental with environmental package air + +URI: [mixs.vocab:AirME](https://w3id.org/mixs/vocab/AirME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Air]^-[AirME],[Air],[ME]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMigsOrg.md b/mixs6/AirMigsOrg.md new file mode 100644 index 00000000..dfd17cd8 --- /dev/null +++ b/mixs6/AirMigsOrg.md @@ -0,0 +1,355 @@ + +# Class: AirMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package air + +URI: [mixs.vocab:AirMIGSOrg](https://w3id.org/mixs/vocab/AirMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Air]^-[AirMIGSOrg],[Air],[MIGSOrg]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMimag.md b/mixs6/AirMimag.md new file mode 100644 index 00000000..fea24eca --- /dev/null +++ b/mixs6/AirMimag.md @@ -0,0 +1,410 @@ + +# Class: AirMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package air + +URI: [mixs.vocab:AirMIMAG](https://w3id.org/mixs/vocab/AirMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Air]^-[AirMIMAG],[Air],[MIMAG]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMisag.md b/mixs6/AirMisag.md new file mode 100644 index 00000000..94dac860 --- /dev/null +++ b/mixs6/AirMisag.md @@ -0,0 +1,415 @@ + +# Class: AirMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package air + +URI: [mixs.vocab:AirMISAG](https://w3id.org/mixs/vocab/AirMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Air]^-[AirMISAG],[Air],[MISAG]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMiuvig.md b/mixs6/AirMiuvig.md new file mode 100644 index 00000000..54689c55 --- /dev/null +++ b/mixs6/AirMiuvig.md @@ -0,0 +1,485 @@ + +# Class: AirMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package air + +URI: [mixs.vocab:AirMIUVIG](https://w3id.org/mixs/vocab/AirMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Air]^-[AirMIUVIG],[Air],[MIUVIG]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/ArchStrucEnum.md b/mixs6/ArchStrucEnum.md new file mode 100644 index 00000000..06972db2 --- /dev/null +++ b/mixs6/ArchStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: arch_struc_enum + + + + +URI: [mixs.vocab:arch_struc_enum](https://w3id.org/mixs/vocab/arch_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/AssemblyQualEnum.md b/mixs6/AssemblyQualEnum.md new file mode 100644 index 00000000..20827320 --- /dev/null +++ b/mixs6/AssemblyQualEnum.md @@ -0,0 +1,19 @@ + +# Enum: assembly_qual_enum + + + + +URI: [mixs.vocab:assembly_qual_enum](https://w3id.org/mixs/vocab/assembly_qual_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BinParamEnum.md b/mixs6/BinParamEnum.md new file mode 100644 index 00000000..24138fc6 --- /dev/null +++ b/mixs6/BinParamEnum.md @@ -0,0 +1,19 @@ + +# Enum: bin_param_enum + + + + +URI: [mixs.vocab:bin_param_enum](https://w3id.org/mixs/vocab/bin_param_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BinSoftwareEnum.md b/mixs6/BinSoftwareEnum.md new file mode 100644 index 00000000..7eb39477 --- /dev/null +++ b/mixs6/BinSoftwareEnum.md @@ -0,0 +1,19 @@ + +# Enum: bin_software_enum + + + + +URI: [mixs.vocab:bin_software_enum](https://w3id.org/mixs/vocab/bin_software_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BiolStatEnum.md b/mixs6/BiolStatEnum.md new file mode 100644 index 00000000..115e7238 --- /dev/null +++ b/mixs6/BiolStatEnum.md @@ -0,0 +1,19 @@ + +# Enum: biol_stat_enum + + + + +URI: [mixs.vocab:biol_stat_enum](https://w3id.org/mixs/vocab/biol_stat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BioticRelationshipEnum.md b/mixs6/BioticRelationshipEnum.md new file mode 100644 index 00000000..d1f48423 --- /dev/null +++ b/mixs6/BioticRelationshipEnum.md @@ -0,0 +1,19 @@ + +# Enum: biotic_relationship_enum + + + + +URI: [mixs.vocab:biotic_relationship_enum](https://w3id.org/mixs/vocab/biotic_relationship_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuildDocsEnum.md b/mixs6/BuildDocsEnum.md new file mode 100644 index 00000000..c15bca12 --- /dev/null +++ b/mixs6/BuildDocsEnum.md @@ -0,0 +1,19 @@ + +# Enum: build_docs_enum + + + + +URI: [mixs.vocab:build_docs_enum](https://w3id.org/mixs/vocab/build_docs_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuildOccupTypeEnum.md b/mixs6/BuildOccupTypeEnum.md new file mode 100644 index 00000000..e30cc7ef --- /dev/null +++ b/mixs6/BuildOccupTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: build_occup_type_enum + + + + +URI: [mixs.vocab:build_occup_type_enum](https://w3id.org/mixs/vocab/build_occup_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuildingSettingEnum.md b/mixs6/BuildingSettingEnum.md new file mode 100644 index 00000000..05422a26 --- /dev/null +++ b/mixs6/BuildingSettingEnum.md @@ -0,0 +1,19 @@ + +# Enum: building_setting_enum + + + + +URI: [mixs.vocab:building_setting_enum](https://w3id.org/mixs/vocab/building_setting_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuiltEnvironment.md b/mixs6/BuiltEnvironment.md new file mode 100644 index 00000000..a2251412 --- /dev/null +++ b/mixs6/BuiltEnvironment.md @@ -0,0 +1,709 @@ + +# Class: BuiltEnvironment + + +built environment + +URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIUVIG],[BuiltEnvironmentMISAG],[BuiltEnvironmentMIMARKSSurvey],[BuiltEnvironmentMIMARKSSpecimen],[BuiltEnvironmentMIMAG],[BuiltEnvironmentMIGSVirus],[BuiltEnvironmentMIGSPlant],[BuiltEnvironmentMIGSOrg],[BuiltEnvironmentMIGSEukaryote],[BuiltEnvironmentMIGSBacteria],[BuiltEnvironmentME],[QuantityValue]OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMIGSBacteria.md b/mixs6/BuiltEnvironmentMIGSBacteria.md new file mode 100644 index 00000000..357c7377 --- /dev/null +++ b/mixs6/BuiltEnvironmentMIGSBacteria.md @@ -0,0 +1,940 @@ + +# Class: BuiltEnvironmentMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSBacteria],[BuiltEnvironment]^-[BuiltEnvironmentMIGSBacteria],[BuiltEnvironment],[MIGSBacteria]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIGSEukaryote.md b/mixs6/BuiltEnvironmentMIGSEukaryote.md new file mode 100644 index 00000000..956bd9e5 --- /dev/null +++ b/mixs6/BuiltEnvironmentMIGSEukaryote.md @@ -0,0 +1,940 @@ + +# Class: BuiltEnvironmentMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSEukaryote],[BuiltEnvironment]^-[BuiltEnvironmentMIGSEukaryote],[BuiltEnvironment],[MIGSEukaryote]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIGSPlant.md b/mixs6/BuiltEnvironmentMIGSPlant.md new file mode 100644 index 00000000..ad15194b --- /dev/null +++ b/mixs6/BuiltEnvironmentMIGSPlant.md @@ -0,0 +1,910 @@ + +# Class: BuiltEnvironmentMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSPlant],[BuiltEnvironment]^-[BuiltEnvironmentMIGSPlant],[BuiltEnvironment],[MIGSPlant]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIGSVirus.md b/mixs6/BuiltEnvironmentMIGSVirus.md new file mode 100644 index 00000000..c17b8b74 --- /dev/null +++ b/mixs6/BuiltEnvironmentMIGSVirus.md @@ -0,0 +1,935 @@ + +# Class: BuiltEnvironmentMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSVirus],[BuiltEnvironment]^-[BuiltEnvironmentMIGSVirus],[BuiltEnvironment],[MIGSVirus]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/BuiltEnvironmentMIMARKSSpecimen.md b/mixs6/BuiltEnvironmentMIMARKSSpecimen.md new file mode 100644 index 00000000..a007bd0a --- /dev/null +++ b/mixs6/BuiltEnvironmentMIMARKSSpecimen.md @@ -0,0 +1,860 @@ + +# Class: BuiltEnvironmentMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSpecimen],[BuiltEnvironment],[MIMARKSSpecimen]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIMARKSSurvey.md b/mixs6/BuiltEnvironmentMIMARKSSurvey.md new file mode 100644 index 00000000..1fa95f7e --- /dev/null +++ b/mixs6/BuiltEnvironmentMIMARKSSurvey.md @@ -0,0 +1,840 @@ + +# Class: BuiltEnvironmentMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSurvey],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSurvey],[BuiltEnvironment],[MIMARKSSurvey]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMe.md b/mixs6/BuiltEnvironmentMe.md new file mode 100644 index 00000000..fcdc2c32 --- /dev/null +++ b/mixs6/BuiltEnvironmentMe.md @@ -0,0 +1,875 @@ + +# Class: BuiltEnvironmentME + + +Combinatorial checklist Metagenome or Environmental with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmentME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[ME],[BuiltEnvironment]^-[BuiltEnvironmentME],[BuiltEnvironment],[ME]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsOrg.md b/mixs6/BuiltEnvironmentMigsOrg.md new file mode 100644 index 00000000..9869e4b2 --- /dev/null +++ b/mixs6/BuiltEnvironmentMigsOrg.md @@ -0,0 +1,895 @@ + +# Class: BuiltEnvironmentMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSOrg],[BuiltEnvironment]^-[BuiltEnvironmentMIGSOrg],[BuiltEnvironment],[MIGSOrg]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMimag.md b/mixs6/BuiltEnvironmentMimag.md new file mode 100644 index 00000000..9f3c29db --- /dev/null +++ b/mixs6/BuiltEnvironmentMimag.md @@ -0,0 +1,950 @@ + +# Class: BuiltEnvironmentMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMAG],[BuiltEnvironment]^-[BuiltEnvironmentMIMAG],[BuiltEnvironment],[MIMAG]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMisag.md b/mixs6/BuiltEnvironmentMisag.md new file mode 100644 index 00000000..01391baf --- /dev/null +++ b/mixs6/BuiltEnvironmentMisag.md @@ -0,0 +1,955 @@ + +# Class: BuiltEnvironmentMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnvironmentMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MISAG],[BuiltEnvironment]^-[BuiltEnvironmentMISAG],[BuiltEnvironment],[MISAG]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMiuvig.md b/mixs6/BuiltEnvironmentMiuvig.md new file mode 100644 index 00000000..f0f39932 --- /dev/null +++ b/mixs6/BuiltEnvironmentMiuvig.md @@ -0,0 +1,1025 @@ + +# Class: BuiltEnvironmentMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnvironmentMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIUVIG],[BuiltEnvironment]^-[BuiltEnvironmentMIUVIG],[BuiltEnvironment],[MIUVIG]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [Date](types/Date.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/CeilCondEnum.md b/mixs6/CeilCondEnum.md new file mode 100644 index 00000000..00363aa1 --- /dev/null +++ b/mixs6/CeilCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_cond_enum + + + + +URI: [mixs.vocab:ceil_cond_enum](https://w3id.org/mixs/vocab/ceil_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/CeilFinishMatEnum.md b/mixs6/CeilFinishMatEnum.md new file mode 100644 index 00000000..866f5463 --- /dev/null +++ b/mixs6/CeilFinishMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_finish_mat_enum + + + + +URI: [mixs.vocab:ceil_finish_mat_enum](https://w3id.org/mixs/vocab/ceil_finish_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/CeilTextureEnum.md b/mixs6/CeilTextureEnum.md new file mode 100644 index 00000000..22812a2d --- /dev/null +++ b/mixs6/CeilTextureEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_texture_enum + + + + +URI: [mixs.vocab:ceil_texture_enum](https://w3id.org/mixs/vocab/ceil_texture_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/CeilTypeEnum.md b/mixs6/CeilTypeEnum.md new file mode 100644 index 00000000..73773347 --- /dev/null +++ b/mixs6/CeilTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_type_enum + + + + +URI: [mixs.vocab:ceil_type_enum](https://w3id.org/mixs/vocab/ceil_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ComplApprEnum.md b/mixs6/ComplApprEnum.md new file mode 100644 index 00000000..7c5b3760 --- /dev/null +++ b/mixs6/ComplApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: compl_appr_enum + + + + +URI: [mixs.vocab:compl_appr_enum](https://w3id.org/mixs/vocab/compl_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ComplScoreEnum.md b/mixs6/ComplScoreEnum.md new file mode 100644 index 00000000..1ee12a34 --- /dev/null +++ b/mixs6/ComplScoreEnum.md @@ -0,0 +1,19 @@ + +# Enum: compl_score_enum + + + + +URI: [mixs.vocab:compl_score_enum](https://w3id.org/mixs/vocab/compl_score_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ContamScreenParamEnum.md b/mixs6/ContamScreenParamEnum.md new file mode 100644 index 00000000..2a3c2fbc --- /dev/null +++ b/mixs6/ContamScreenParamEnum.md @@ -0,0 +1,19 @@ + +# Enum: contam_screen_param_enum + + + + +URI: [mixs.vocab:contam_screen_param_enum](https://w3id.org/mixs/vocab/contam_screen_param_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Core.md b/mixs6/Core.md new file mode 100644 index 00000000..78978bb0 --- /dev/null +++ b/mixs6/Core.md @@ -0,0 +1,395 @@ + +# Class: Core + + +Core package. Do not use this directly, this is used to build other packages + +URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue]OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 5 liter None + * [sample_collect_device](sample_collect_device.md) OPT + * Description: The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). + * range: [String](types/String.md) + * Example: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] None + * [sample_collect_method](sample_collect_method.md) OPT + * Description: The method employed for collecting the sample. + * range: [String](types/String.md) + * Example: swabbing None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: ISDsoil1 None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None diff --git a/mixs6/CurLandUseEnum.md b/mixs6/CurLandUseEnum.md new file mode 100644 index 00000000..9ac62b25 --- /dev/null +++ b/mixs6/CurLandUseEnum.md @@ -0,0 +1,19 @@ + +# Enum: cur_land_use_enum + + + + +URI: [mixs.vocab:cur_land_use_enum](https://w3id.org/mixs/vocab/cur_land_use_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DecontamSoftwareEnum.md b/mixs6/DecontamSoftwareEnum.md new file mode 100644 index 00000000..8830f0da --- /dev/null +++ b/mixs6/DecontamSoftwareEnum.md @@ -0,0 +1,19 @@ + +# Enum: decontam_software_enum + + + + +URI: [mixs.vocab:decontam_software_enum](https://w3id.org/mixs/vocab/decontam_software_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DeposEnvEnum.md b/mixs6/DeposEnvEnum.md new file mode 100644 index 00000000..2b432441 --- /dev/null +++ b/mixs6/DeposEnvEnum.md @@ -0,0 +1,19 @@ + +# Enum: depos_env_enum + + + + +URI: [mixs.vocab:depos_env_enum](https://w3id.org/mixs/vocab/depos_env_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DominantHandEnum.md b/mixs6/DominantHandEnum.md new file mode 100644 index 00000000..a9fa1d26 --- /dev/null +++ b/mixs6/DominantHandEnum.md @@ -0,0 +1,19 @@ + +# Enum: dominant_hand_enum + + + + +URI: [mixs.vocab:dominant_hand_enum](https://w3id.org/mixs/vocab/dominant_hand_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorCompTypeEnum.md b/mixs6/DoorCompTypeEnum.md new file mode 100644 index 00000000..8d12d7df --- /dev/null +++ b/mixs6/DoorCompTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_comp_type_enum + + + + +URI: [mixs.vocab:door_comp_type_enum](https://w3id.org/mixs/vocab/door_comp_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorCondEnum.md b/mixs6/DoorCondEnum.md new file mode 100644 index 00000000..3515588e --- /dev/null +++ b/mixs6/DoorCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_cond_enum + + + + +URI: [mixs.vocab:door_cond_enum](https://w3id.org/mixs/vocab/door_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorDirectEnum.md b/mixs6/DoorDirectEnum.md new file mode 100644 index 00000000..be251896 --- /dev/null +++ b/mixs6/DoorDirectEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_direct_enum + + + + +URI: [mixs.vocab:door_direct_enum](https://w3id.org/mixs/vocab/door_direct_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorLocEnum.md b/mixs6/DoorLocEnum.md new file mode 100644 index 00000000..26fff28d --- /dev/null +++ b/mixs6/DoorLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_loc_enum + + + + +URI: [mixs.vocab:door_loc_enum](https://w3id.org/mixs/vocab/door_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorMatEnum.md b/mixs6/DoorMatEnum.md new file mode 100644 index 00000000..a1087468 --- /dev/null +++ b/mixs6/DoorMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_mat_enum + + + + +URI: [mixs.vocab:door_mat_enum](https://w3id.org/mixs/vocab/door_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorMoveEnum.md b/mixs6/DoorMoveEnum.md new file mode 100644 index 00000000..66920cc7 --- /dev/null +++ b/mixs6/DoorMoveEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_move_enum + + + + +URI: [mixs.vocab:door_move_enum](https://w3id.org/mixs/vocab/door_move_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorTypeEnum.md b/mixs6/DoorTypeEnum.md new file mode 100644 index 00000000..42f85a21 --- /dev/null +++ b/mixs6/DoorTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_type_enum + + + + +URI: [mixs.vocab:door_type_enum](https://w3id.org/mixs/vocab/door_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorTypeMetalEnum.md b/mixs6/DoorTypeMetalEnum.md new file mode 100644 index 00000000..72f827ce --- /dev/null +++ b/mixs6/DoorTypeMetalEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_type_metal_enum + + + + +URI: [mixs.vocab:door_type_metal_enum](https://w3id.org/mixs/vocab/door_type_metal_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorTypeWoodEnum.md b/mixs6/DoorTypeWoodEnum.md new file mode 100644 index 00000000..3955d511 --- /dev/null +++ b/mixs6/DoorTypeWoodEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_type_wood_enum + + + + +URI: [mixs.vocab:door_type_wood_enum](https://w3id.org/mixs/vocab/door_type_wood_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DrainageClassEnum.md b/mixs6/DrainageClassEnum.md new file mode 100644 index 00000000..d014a33b --- /dev/null +++ b/mixs6/DrainageClassEnum.md @@ -0,0 +1,19 @@ + +# Enum: drainage_class_enum + + + + +URI: [mixs.vocab:drainage_class_enum](https://w3id.org/mixs/vocab/drainage_class_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DrawingsEnum.md b/mixs6/DrawingsEnum.md new file mode 100644 index 00000000..cf8f0401 --- /dev/null +++ b/mixs6/DrawingsEnum.md @@ -0,0 +1,19 @@ + +# Enum: drawings_enum + + + + +URI: [mixs.vocab:drawings_enum](https://w3id.org/mixs/vocab/drawings_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DrugUsageEnum.md b/mixs6/DrugUsageEnum.md new file mode 100644 index 00000000..43353654 --- /dev/null +++ b/mixs6/DrugUsageEnum.md @@ -0,0 +1,19 @@ + +# Enum: drug_usage_enum + + + + +URI: [mixs.vocab:drug_usage_enum](https://w3id.org/mixs/vocab/drug_usage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/EnvPackageEnum.md b/mixs6/EnvPackageEnum.md new file mode 100644 index 00000000..5bcb16e7 --- /dev/null +++ b/mixs6/EnvPackageEnum.md @@ -0,0 +1,19 @@ + +# Enum: env_package_enum + + + + +URI: [mixs.vocab:env_package_enum](https://w3id.org/mixs/vocab/env_package_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ExtWallOrientEnum.md b/mixs6/ExtWallOrientEnum.md new file mode 100644 index 00000000..019a00f3 --- /dev/null +++ b/mixs6/ExtWallOrientEnum.md @@ -0,0 +1,19 @@ + +# Enum: ext_wall_orient_enum + + + + +URI: [mixs.vocab:ext_wall_orient_enum](https://w3id.org/mixs/vocab/ext_wall_orient_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ExtWindowOrientEnum.md b/mixs6/ExtWindowOrientEnum.md new file mode 100644 index 00000000..6cf9893d --- /dev/null +++ b/mixs6/ExtWindowOrientEnum.md @@ -0,0 +1,19 @@ + +# Enum: ext_window_orient_enum + + + + +URI: [mixs.vocab:ext_window_orient_enum](https://w3id.org/mixs/vocab/ext_window_orient_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FaoClassEnum.md b/mixs6/FaoClassEnum.md new file mode 100644 index 00000000..4c41fd09 --- /dev/null +++ b/mixs6/FaoClassEnum.md @@ -0,0 +1,19 @@ + +# Enum: fao_class_enum + + + + +URI: [mixs.vocab:fao_class_enum](https://w3id.org/mixs/vocab/fao_class_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FilterTypeEnum.md b/mixs6/FilterTypeEnum.md new file mode 100644 index 00000000..14a1bc88 --- /dev/null +++ b/mixs6/FilterTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: filter_type_enum + + + + +URI: [mixs.vocab:filter_type_enum](https://w3id.org/mixs/vocab/filter_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorCondEnum.md b/mixs6/FloorCondEnum.md new file mode 100644 index 00000000..fdb715ab --- /dev/null +++ b/mixs6/FloorCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_cond_enum + + + + +URI: [mixs.vocab:floor_cond_enum](https://w3id.org/mixs/vocab/floor_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorFinishMatEnum.md b/mixs6/FloorFinishMatEnum.md new file mode 100644 index 00000000..d162ea24 --- /dev/null +++ b/mixs6/FloorFinishMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_finish_mat_enum + + + + +URI: [mixs.vocab:floor_finish_mat_enum](https://w3id.org/mixs/vocab/floor_finish_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorStrucEnum.md b/mixs6/FloorStrucEnum.md new file mode 100644 index 00000000..ffa28c50 --- /dev/null +++ b/mixs6/FloorStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_struc_enum + + + + +URI: [mixs.vocab:floor_struc_enum](https://w3id.org/mixs/vocab/floor_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorWaterMoldEnum.md b/mixs6/FloorWaterMoldEnum.md new file mode 100644 index 00000000..a748764d --- /dev/null +++ b/mixs6/FloorWaterMoldEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_water_mold_enum + + + + +URI: [mixs.vocab:floor_water_mold_enum](https://w3id.org/mixs/vocab/floor_water_mold_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FurnitureEnum.md b/mixs6/FurnitureEnum.md new file mode 100644 index 00000000..1dc61975 --- /dev/null +++ b/mixs6/FurnitureEnum.md @@ -0,0 +1,19 @@ + +# Enum: furniture_enum + + + + +URI: [mixs.vocab:furniture_enum](https://w3id.org/mixs/vocab/furniture_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/GrowthHabitEnum.md b/mixs6/GrowthHabitEnum.md new file mode 100644 index 00000000..3885f19d --- /dev/null +++ b/mixs6/GrowthHabitEnum.md @@ -0,0 +1,19 @@ + +# Enum: growth_habit_enum + + + + +URI: [mixs.vocab:growth_habit_enum](https://w3id.org/mixs/vocab/growth_habit_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HandidnessEnum.md b/mixs6/HandidnessEnum.md new file mode 100644 index 00000000..e668a948 --- /dev/null +++ b/mixs6/HandidnessEnum.md @@ -0,0 +1,19 @@ + +# Enum: handidness_enum + + + + +URI: [mixs.vocab:handidness_enum](https://w3id.org/mixs/vocab/handidness_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HcProducedEnum.md b/mixs6/HcProducedEnum.md new file mode 100644 index 00000000..aee509e6 --- /dev/null +++ b/mixs6/HcProducedEnum.md @@ -0,0 +1,19 @@ + +# Enum: hc_produced_enum + + + + +URI: [mixs.vocab:hc_produced_enum](https://w3id.org/mixs/vocab/hc_produced_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HcrEnum.md b/mixs6/HcrEnum.md new file mode 100644 index 00000000..67994695 --- /dev/null +++ b/mixs6/HcrEnum.md @@ -0,0 +1,19 @@ + +# Enum: hcr_enum + + + + +URI: [mixs.vocab:hcr_enum](https://w3id.org/mixs/vocab/hcr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HcrGeolAgeEnum.md b/mixs6/HcrGeolAgeEnum.md new file mode 100644 index 00000000..c5ce3298 --- /dev/null +++ b/mixs6/HcrGeolAgeEnum.md @@ -0,0 +1,19 @@ + +# Enum: hcr_geol_age_enum + + + + +URI: [mixs.vocab:hcr_geol_age_enum](https://w3id.org/mixs/vocab/hcr_geol_age_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HealthDiseaseStatEnum.md b/mixs6/HealthDiseaseStatEnum.md new file mode 100644 index 00000000..b6c9eb67 --- /dev/null +++ b/mixs6/HealthDiseaseStatEnum.md @@ -0,0 +1,19 @@ + +# Enum: health_disease_stat_enum + + + + +URI: [mixs.vocab:health_disease_stat_enum](https://w3id.org/mixs/vocab/health_disease_stat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HeatCoolTypeEnum.md b/mixs6/HeatCoolTypeEnum.md new file mode 100644 index 00000000..d00438f4 --- /dev/null +++ b/mixs6/HeatCoolTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: heat_cool_type_enum + + + + +URI: [mixs.vocab:heat_cool_type_enum](https://w3id.org/mixs/vocab/heat_cool_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HeatDelivLocEnum.md b/mixs6/HeatDelivLocEnum.md new file mode 100644 index 00000000..70ceedab --- /dev/null +++ b/mixs6/HeatDelivLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: heat_deliv_loc_enum + + + + +URI: [mixs.vocab:heat_deliv_loc_enum](https://w3id.org/mixs/vocab/heat_deliv_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HorizonEnum.md b/mixs6/HorizonEnum.md new file mode 100644 index 00000000..84a3fa5f --- /dev/null +++ b/mixs6/HorizonEnum.md @@ -0,0 +1,19 @@ + +# Enum: horizon_enum + + + + +URI: [mixs.vocab:horizon_enum](https://w3id.org/mixs/vocab/horizon_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Host-associated.md b/mixs6/Host-associated.md new file mode 100644 index 00000000..fc327ca1 --- /dev/null +++ b/mixs6/Host-associated.md @@ -0,0 +1,253 @@ + +# Class: Host-associated + + +host-associated + +URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIUVIG],[Host-associatedMISAG],[Host-associatedMIMARKSSurvey],[Host-associatedMIMARKSSpecimen],[Host-associatedMIMAG],[Host-associatedMIGSVirus],[Host-associatedMIGSPlant],[Host-associatedMIGSOrg],[Host-associatedMIGSEukaryote],[Host-associatedMIGSBacteria],[Host-associatedME],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMIGSBacteria.md b/mixs6/Host-associatedMIGSBacteria.md new file mode 100644 index 00000000..f2ce2577 --- /dev/null +++ b/mixs6/Host-associatedMIGSBacteria.md @@ -0,0 +1,484 @@ + +# Class: Host-associatedMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-associatedMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Host-associated]^-[Host-associatedMIGSBacteria],[Host-associated],[MIGSBacteria]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIGSEukaryote.md b/mixs6/Host-associatedMIGSEukaryote.md new file mode 100644 index 00000000..5d1f64d1 --- /dev/null +++ b/mixs6/Host-associatedMIGSEukaryote.md @@ -0,0 +1,484 @@ + +# Class: Host-associatedMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host-associatedMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Host-associated]^-[Host-associatedMIGSEukaryote],[Host-associated],[MIGSEukaryote]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIGSPlant.md b/mixs6/Host-associatedMIGSPlant.md new file mode 100644 index 00000000..876b342b --- /dev/null +++ b/mixs6/Host-associatedMIGSPlant.md @@ -0,0 +1,454 @@ + +# Class: Host-associatedMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-associatedMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Host-associated]^-[Host-associatedMIGSPlant],[Host-associated],[MIGSPlant]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIGSVirus.md b/mixs6/Host-associatedMIGSVirus.md new file mode 100644 index 00000000..e7acd728 --- /dev/null +++ b/mixs6/Host-associatedMIGSVirus.md @@ -0,0 +1,479 @@ + +# Class: Host-associatedMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-associatedMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Host-associated]^-[Host-associatedMIGSVirus],[Host-associated],[MIGSVirus]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Host-associatedMIMARKSSpecimen.md b/mixs6/Host-associatedMIMARKSSpecimen.md new file mode 100644 index 00000000..315e419a --- /dev/null +++ b/mixs6/Host-associatedMIMARKSSpecimen.md @@ -0,0 +1,404 @@ + +# Class: Host-associatedMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Host-associatedMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Host-associated]^-[Host-associatedMIMARKSSpecimen],[Host-associated],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIMARKSSurvey.md b/mixs6/Host-associatedMIMARKSSurvey.md new file mode 100644 index 00000000..4e66d89d --- /dev/null +++ b/mixs6/Host-associatedMIMARKSSurvey.md @@ -0,0 +1,384 @@ + +# Class: Host-associatedMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host-associatedMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Host-associated]^-[Host-associatedMIMARKSSurvey],[Host-associated],[MIMARKSSurvey]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMe.md b/mixs6/Host-associatedMe.md new file mode 100644 index 00000000..3b8844c2 --- /dev/null +++ b/mixs6/Host-associatedMe.md @@ -0,0 +1,419 @@ + +# Class: Host-associatedME + + +Combinatorial checklist Metagenome or Environmental with environmental package host-associated + +URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Host-associated]^-[Host-associatedME],[Host-associated],[ME]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsOrg.md b/mixs6/Host-associatedMigsOrg.md new file mode 100644 index 00000000..302800e1 --- /dev/null +++ b/mixs6/Host-associatedMigsOrg.md @@ -0,0 +1,439 @@ + +# Class: Host-associatedMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associatedMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Host-associated]^-[Host-associatedMIGSOrg],[Host-associated],[MIGSOrg]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMimag.md b/mixs6/Host-associatedMimag.md new file mode 100644 index 00000000..0ec00560 --- /dev/null +++ b/mixs6/Host-associatedMimag.md @@ -0,0 +1,494 @@ + +# Class: Host-associatedMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associatedMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Host-associated]^-[Host-associatedMIMAG],[Host-associated],[MIMAG]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMisag.md b/mixs6/Host-associatedMisag.md new file mode 100644 index 00000000..26f60b0a --- /dev/null +++ b/mixs6/Host-associatedMisag.md @@ -0,0 +1,499 @@ + +# Class: Host-associatedMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associatedMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Host-associated]^-[Host-associatedMISAG],[Host-associated],[MISAG]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMiuvig.md b/mixs6/Host-associatedMiuvig.md new file mode 100644 index 00000000..8186d515 --- /dev/null +++ b/mixs6/Host-associatedMiuvig.md @@ -0,0 +1,569 @@ + +# Class: Host-associatedMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associatedMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Host-associated]^-[Host-associatedMIUVIG],[Host-associated],[MIUVIG]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HostPredApprEnum.md b/mixs6/HostPredApprEnum.md new file mode 100644 index 00000000..6c853164 --- /dev/null +++ b/mixs6/HostPredApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: host_pred_appr_enum + + + + +URI: [mixs.vocab:host_pred_appr_enum](https://w3id.org/mixs/vocab/host_pred_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HostSexEnum.md b/mixs6/HostSexEnum.md new file mode 100644 index 00000000..890f4a59 --- /dev/null +++ b/mixs6/HostSexEnum.md @@ -0,0 +1,19 @@ + +# Enum: host_sex_enum + + + + +URI: [mixs.vocab:host_sex_enum](https://w3id.org/mixs/vocab/host_sex_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Human-associated.md b/mixs6/Human-associated.md new file mode 100644 index 00000000..eb50f697 --- /dev/null +++ b/mixs6/Human-associated.md @@ -0,0 +1,273 @@ + +# Class: Human-associated + + +human-associated + +URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIUVIG],[Human-associatedMISAG],[Human-associatedMIMARKSSurvey],[Human-associatedMIMARKSSpecimen],[Human-associatedMIMAG],[Human-associatedMIGSVirus],[Human-associatedMIGSPlant],[Human-associatedMIGSOrg],[Human-associatedMIGSEukaryote],[Human-associatedMIGSBacteria],[Human-associatedME],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMIGSBacteria.md b/mixs6/Human-associatedMIGSBacteria.md new file mode 100644 index 00000000..8f4f475d --- /dev/null +++ b/mixs6/Human-associatedMIGSBacteria.md @@ -0,0 +1,504 @@ + +# Class: Human-associatedMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Human-associatedMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-associated]^-[Human-associatedMIGSBacteria],[Human-associated],[MIGSBacteria]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIGSEukaryote.md b/mixs6/Human-associatedMIGSEukaryote.md new file mode 100644 index 00000000..4e5a9b22 --- /dev/null +++ b/mixs6/Human-associatedMIGSEukaryote.md @@ -0,0 +1,504 @@ + +# Class: Human-associatedMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Human-associatedMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-associated]^-[Human-associatedMIGSEukaryote],[Human-associated],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIGSPlant.md b/mixs6/Human-associatedMIGSPlant.md new file mode 100644 index 00000000..00e67271 --- /dev/null +++ b/mixs6/Human-associatedMIGSPlant.md @@ -0,0 +1,474 @@ + +# Class: Human-associatedMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-associatedMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-associated]^-[Human-associatedMIGSPlant],[Human-associated],[MIGSPlant]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIGSVirus.md b/mixs6/Human-associatedMIGSVirus.md new file mode 100644 index 00000000..0f7274a4 --- /dev/null +++ b/mixs6/Human-associatedMIGSVirus.md @@ -0,0 +1,499 @@ + +# Class: Human-associatedMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-associatedMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-associated]^-[Human-associatedMIGSVirus],[Human-associated],[MIGSVirus]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-associatedMIMARKSSpecimen.md b/mixs6/Human-associatedMIMARKSSpecimen.md new file mode 100644 index 00000000..52921041 --- /dev/null +++ b/mixs6/Human-associatedMIMARKSSpecimen.md @@ -0,0 +1,424 @@ + +# Class: Human-associatedMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-associatedMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-associated]^-[Human-associatedMIMARKSSpecimen],[Human-associated],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIMARKSSurvey.md b/mixs6/Human-associatedMIMARKSSurvey.md new file mode 100644 index 00000000..ff7c67a3 --- /dev/null +++ b/mixs6/Human-associatedMIMARKSSurvey.md @@ -0,0 +1,404 @@ + +# Class: Human-associatedMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-associatedMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-associated]^-[Human-associatedMIMARKSSurvey],[Human-associated],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMe.md b/mixs6/Human-associatedMe.md new file mode 100644 index 00000000..e90fad30 --- /dev/null +++ b/mixs6/Human-associatedMe.md @@ -0,0 +1,439 @@ + +# Class: Human-associatedME + + +Combinatorial checklist Metagenome or Environmental with environmental package human-associated + +URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associatedME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-associated]^-[Human-associatedME],[Human-associated],[ME]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsOrg.md b/mixs6/Human-associatedMigsOrg.md new file mode 100644 index 00000000..670ff68f --- /dev/null +++ b/mixs6/Human-associatedMigsOrg.md @@ -0,0 +1,459 @@ + +# Class: Human-associatedMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-associatedMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-associated]^-[Human-associatedMIGSOrg],[Human-associated],[MIGSOrg]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMimag.md b/mixs6/Human-associatedMimag.md new file mode 100644 index 00000000..096a8afa --- /dev/null +++ b/mixs6/Human-associatedMimag.md @@ -0,0 +1,514 @@ + +# Class: Human-associatedMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associatedMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-associated]^-[Human-associatedMIMAG],[Human-associated],[MIMAG]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMisag.md b/mixs6/Human-associatedMisag.md new file mode 100644 index 00000000..51557f35 --- /dev/null +++ b/mixs6/Human-associatedMisag.md @@ -0,0 +1,519 @@ + +# Class: Human-associatedMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associatedMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-associated]^-[Human-associatedMISAG],[Human-associated],[MISAG]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMiuvig.md b/mixs6/Human-associatedMiuvig.md new file mode 100644 index 00000000..3917a641 --- /dev/null +++ b/mixs6/Human-associatedMiuvig.md @@ -0,0 +1,589 @@ + +# Class: Human-associatedMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-associatedMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-associated]^-[Human-associatedMIUVIG],[Human-associated],[MIUVIG]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gut.md b/mixs6/Human-gut.md new file mode 100644 index 00000000..c1e67896 --- /dev/null +++ b/mixs6/Human-gut.md @@ -0,0 +1,209 @@ + +# Class: Human-gut + + +human-gut + +URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIUVIG],[Human-gutMISAG],[Human-gutMIMARKSSurvey],[Human-gutMIMARKSSpecimen],[Human-gutMIMAG],[Human-gutMIGSVirus],[Human-gutMIGSPlant],[Human-gutMIGSOrg],[Human-gutMIGSEukaryote],[Human-gutMIGSBacteria],[Human-gutME],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMIGSBacteria.md b/mixs6/Human-gutMIGSBacteria.md new file mode 100644 index 00000000..91028283 --- /dev/null +++ b/mixs6/Human-gutMIGSBacteria.md @@ -0,0 +1,440 @@ + +# Class: Human-gutMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSBacteria](https://w3id.org/mixs/vocab/Human-gutMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-gut]^-[Human-gutMIGSBacteria],[Human-gut],[MIGSBacteria]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIGSEukaryote.md b/mixs6/Human-gutMIGSEukaryote.md new file mode 100644 index 00000000..e716259e --- /dev/null +++ b/mixs6/Human-gutMIGSEukaryote.md @@ -0,0 +1,440 @@ + +# Class: Human-gutMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSEukaryote](https://w3id.org/mixs/vocab/Human-gutMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-gut]^-[Human-gutMIGSEukaryote],[Human-gut],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIGSPlant.md b/mixs6/Human-gutMIGSPlant.md new file mode 100644 index 00000000..52024785 --- /dev/null +++ b/mixs6/Human-gutMIGSPlant.md @@ -0,0 +1,410 @@ + +# Class: Human-gutMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSPlant](https://w3id.org/mixs/vocab/Human-gutMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-gut]^-[Human-gutMIGSPlant],[Human-gut],[MIGSPlant]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIGSVirus.md b/mixs6/Human-gutMIGSVirus.md new file mode 100644 index 00000000..56c17587 --- /dev/null +++ b/mixs6/Human-gutMIGSVirus.md @@ -0,0 +1,435 @@ + +# Class: Human-gutMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSVirus](https://w3id.org/mixs/vocab/Human-gutMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-gut]^-[Human-gutMIGSVirus],[Human-gut],[MIGSVirus]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-gutMIMARKSSpecimen.md b/mixs6/Human-gutMIMARKSSpecimen.md new file mode 100644 index 00000000..7c6fb2ae --- /dev/null +++ b/mixs6/Human-gutMIMARKSSpecimen.md @@ -0,0 +1,360 @@ + +# Class: Human-gutMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-gutMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-gut]^-[Human-gutMIMARKSSpecimen],[Human-gut],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIMARKSSurvey.md b/mixs6/Human-gutMIMARKSSurvey.md new file mode 100644 index 00000000..f9ff5f5f --- /dev/null +++ b/mixs6/Human-gutMIMARKSSurvey.md @@ -0,0 +1,340 @@ + +# Class: Human-gutMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-gutMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-gut]^-[Human-gutMIMARKSSurvey],[Human-gut],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMe.md b/mixs6/Human-gutMe.md new file mode 100644 index 00000000..45316412 --- /dev/null +++ b/mixs6/Human-gutMe.md @@ -0,0 +1,375 @@ + +# Class: Human-gutME + + +Combinatorial checklist Metagenome or Environmental with environmental package human-gut + +URI: [mixs.vocab:Human-gutME](https://w3id.org/mixs/vocab/Human-gutME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-gut]^-[Human-gutME],[Human-gut],[ME]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsOrg.md b/mixs6/Human-gutMigsOrg.md new file mode 100644 index 00000000..ddcf75d7 --- /dev/null +++ b/mixs6/Human-gutMigsOrg.md @@ -0,0 +1,395 @@ + +# Class: Human-gutMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSOrg](https://w3id.org/mixs/vocab/Human-gutMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-gut]^-[Human-gutMIGSOrg],[Human-gut],[MIGSOrg]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMimag.md b/mixs6/Human-gutMimag.md new file mode 100644 index 00000000..1290868f --- /dev/null +++ b/mixs6/Human-gutMimag.md @@ -0,0 +1,450 @@ + +# Class: Human-gutMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-gut]^-[Human-gutMIMAG],[Human-gut],[MIMAG]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMisag.md b/mixs6/Human-gutMisag.md new file mode 100644 index 00000000..26adb92d --- /dev/null +++ b/mixs6/Human-gutMisag.md @@ -0,0 +1,455 @@ + +# Class: Human-gutMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-gut + +URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-gut]^-[Human-gutMISAG],[Human-gut],[MISAG]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMiuvig.md b/mixs6/Human-gutMiuvig.md new file mode 100644 index 00000000..3d6f8aab --- /dev/null +++ b/mixs6/Human-gutMiuvig.md @@ -0,0 +1,525 @@ + +# Class: Human-gutMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIUVIG](https://w3id.org/mixs/vocab/Human-gutMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-gut]^-[Human-gutMIUVIG],[Human-gut],[MIUVIG]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oral.md b/mixs6/Human-oral.md new file mode 100644 index 00000000..c1f87f0e --- /dev/null +++ b/mixs6/Human-oral.md @@ -0,0 +1,205 @@ + +# Class: Human-oral + + +human-oral + +URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIUVIG],[Human-oralMISAG],[Human-oralMIMARKSSurvey],[Human-oralMIMARKSSpecimen],[Human-oralMIMAG],[Human-oralMIGSVirus],[Human-oralMIGSPlant],[Human-oralMIGSOrg],[Human-oralMIGSEukaryote],[Human-oralMIGSBacteria],[Human-oralME],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMIGSBacteria.md b/mixs6/Human-oralMIGSBacteria.md new file mode 100644 index 00000000..46bf8fc4 --- /dev/null +++ b/mixs6/Human-oralMIGSBacteria.md @@ -0,0 +1,436 @@ + +# Class: Human-oralMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSBacteria](https://w3id.org/mixs/vocab/Human-oralMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-oral]^-[Human-oralMIGSBacteria],[Human-oral],[MIGSBacteria]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIGSEukaryote.md b/mixs6/Human-oralMIGSEukaryote.md new file mode 100644 index 00000000..bb30d3d2 --- /dev/null +++ b/mixs6/Human-oralMIGSEukaryote.md @@ -0,0 +1,436 @@ + +# Class: Human-oralMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSEukaryote](https://w3id.org/mixs/vocab/Human-oralMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-oral]^-[Human-oralMIGSEukaryote],[Human-oral],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIGSPlant.md b/mixs6/Human-oralMIGSPlant.md new file mode 100644 index 00000000..e59b706e --- /dev/null +++ b/mixs6/Human-oralMIGSPlant.md @@ -0,0 +1,406 @@ + +# Class: Human-oralMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSPlant](https://w3id.org/mixs/vocab/Human-oralMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-oral]^-[Human-oralMIGSPlant],[Human-oral],[MIGSPlant]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIGSVirus.md b/mixs6/Human-oralMIGSVirus.md new file mode 100644 index 00000000..13edcace --- /dev/null +++ b/mixs6/Human-oralMIGSVirus.md @@ -0,0 +1,431 @@ + +# Class: Human-oralMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSVirus](https://w3id.org/mixs/vocab/Human-oralMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-oral]^-[Human-oralMIGSVirus],[Human-oral],[MIGSVirus]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-oralMIMARKSSpecimen.md b/mixs6/Human-oralMIMARKSSpecimen.md new file mode 100644 index 00000000..0aa0b8af --- /dev/null +++ b/mixs6/Human-oralMIMARKSSpecimen.md @@ -0,0 +1,356 @@ + +# Class: Human-oralMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-oralMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-oral]^-[Human-oralMIMARKSSpecimen],[Human-oral],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIMARKSSurvey.md b/mixs6/Human-oralMIMARKSSurvey.md new file mode 100644 index 00000000..959f5e45 --- /dev/null +++ b/mixs6/Human-oralMIMARKSSurvey.md @@ -0,0 +1,336 @@ + +# Class: Human-oralMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-oralMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-oral]^-[Human-oralMIMARKSSurvey],[Human-oral],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMe.md b/mixs6/Human-oralMe.md new file mode 100644 index 00000000..1cc994ff --- /dev/null +++ b/mixs6/Human-oralMe.md @@ -0,0 +1,371 @@ + +# Class: Human-oralME + + +Combinatorial checklist Metagenome or Environmental with environmental package human-oral + +URI: [mixs.vocab:Human-oralME](https://w3id.org/mixs/vocab/Human-oralME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-oral]^-[Human-oralME],[Human-oral],[ME]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsOrg.md b/mixs6/Human-oralMigsOrg.md new file mode 100644 index 00000000..f2f43fb2 --- /dev/null +++ b/mixs6/Human-oralMigsOrg.md @@ -0,0 +1,391 @@ + +# Class: Human-oralMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSOrg](https://w3id.org/mixs/vocab/Human-oralMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-oral]^-[Human-oralMIGSOrg],[Human-oral],[MIGSOrg]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMimag.md b/mixs6/Human-oralMimag.md new file mode 100644 index 00000000..0b284360 --- /dev/null +++ b/mixs6/Human-oralMimag.md @@ -0,0 +1,446 @@ + +# Class: Human-oralMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-oral]^-[Human-oralMIMAG],[Human-oral],[MIMAG]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMisag.md b/mixs6/Human-oralMisag.md new file mode 100644 index 00000000..12a6c368 --- /dev/null +++ b/mixs6/Human-oralMisag.md @@ -0,0 +1,451 @@ + +# Class: Human-oralMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-oral + +URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-oral]^-[Human-oralMISAG],[Human-oral],[MISAG]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMiuvig.md b/mixs6/Human-oralMiuvig.md new file mode 100644 index 00000000..ed3bbd35 --- /dev/null +++ b/mixs6/Human-oralMiuvig.md @@ -0,0 +1,521 @@ + +# Class: Human-oralMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIUVIG](https://w3id.org/mixs/vocab/Human-oralMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-oral]^-[Human-oralMIUVIG],[Human-oral],[MIUVIG]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skin.md b/mixs6/Human-skin.md new file mode 100644 index 00000000..e4b1060c --- /dev/null +++ b/mixs6/Human-skin.md @@ -0,0 +1,209 @@ + +# Class: Human-skin + + +human-skin + +URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIUVIG],[Human-skinMISAG],[Human-skinMIMARKSSurvey],[Human-skinMIMARKSSpecimen],[Human-skinMIMAG],[Human-skinMIGSVirus],[Human-skinMIGSPlant],[Human-skinMIGSOrg],[Human-skinMIGSEukaryote],[Human-skinMIGSBacteria],[Human-skinME],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMIGSBacteria.md b/mixs6/Human-skinMIGSBacteria.md new file mode 100644 index 00000000..10572bf0 --- /dev/null +++ b/mixs6/Human-skinMIGSBacteria.md @@ -0,0 +1,440 @@ + +# Class: Human-skinMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSBacteria](https://w3id.org/mixs/vocab/Human-skinMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-skin]^-[Human-skinMIGSBacteria],[Human-skin],[MIGSBacteria]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIGSEukaryote.md b/mixs6/Human-skinMIGSEukaryote.md new file mode 100644 index 00000000..3fac3d8a --- /dev/null +++ b/mixs6/Human-skinMIGSEukaryote.md @@ -0,0 +1,440 @@ + +# Class: Human-skinMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSEukaryote](https://w3id.org/mixs/vocab/Human-skinMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-skin]^-[Human-skinMIGSEukaryote],[Human-skin],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIGSPlant.md b/mixs6/Human-skinMIGSPlant.md new file mode 100644 index 00000000..58b7ffbd --- /dev/null +++ b/mixs6/Human-skinMIGSPlant.md @@ -0,0 +1,410 @@ + +# Class: Human-skinMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSPlant](https://w3id.org/mixs/vocab/Human-skinMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-skin]^-[Human-skinMIGSPlant],[Human-skin],[MIGSPlant]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIGSVirus.md b/mixs6/Human-skinMIGSVirus.md new file mode 100644 index 00000000..be0e0604 --- /dev/null +++ b/mixs6/Human-skinMIGSVirus.md @@ -0,0 +1,435 @@ + +# Class: Human-skinMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSVirus](https://w3id.org/mixs/vocab/Human-skinMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-skin]^-[Human-skinMIGSVirus],[Human-skin],[MIGSVirus]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-skinMIMARKSSpecimen.md b/mixs6/Human-skinMIMARKSSpecimen.md new file mode 100644 index 00000000..2794412e --- /dev/null +++ b/mixs6/Human-skinMIMARKSSpecimen.md @@ -0,0 +1,360 @@ + +# Class: Human-skinMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-skinMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-skin]^-[Human-skinMIMARKSSpecimen],[Human-skin],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIMARKSSurvey.md b/mixs6/Human-skinMIMARKSSurvey.md new file mode 100644 index 00000000..b4b0ee30 --- /dev/null +++ b/mixs6/Human-skinMIMARKSSurvey.md @@ -0,0 +1,340 @@ + +# Class: Human-skinMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-skinMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-skin]^-[Human-skinMIMARKSSurvey],[Human-skin],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMe.md b/mixs6/Human-skinMe.md new file mode 100644 index 00000000..264dd4ec --- /dev/null +++ b/mixs6/Human-skinMe.md @@ -0,0 +1,375 @@ + +# Class: Human-skinME + + +Combinatorial checklist Metagenome or Environmental with environmental package human-skin + +URI: [mixs.vocab:Human-skinME](https://w3id.org/mixs/vocab/Human-skinME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-skin]^-[Human-skinME],[Human-skin],[ME]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsOrg.md b/mixs6/Human-skinMigsOrg.md new file mode 100644 index 00000000..f32997ec --- /dev/null +++ b/mixs6/Human-skinMigsOrg.md @@ -0,0 +1,395 @@ + +# Class: Human-skinMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSOrg](https://w3id.org/mixs/vocab/Human-skinMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-skin]^-[Human-skinMIGSOrg],[Human-skin],[MIGSOrg]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMimag.md b/mixs6/Human-skinMimag.md new file mode 100644 index 00000000..3f44e568 --- /dev/null +++ b/mixs6/Human-skinMimag.md @@ -0,0 +1,450 @@ + +# Class: Human-skinMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-skin]^-[Human-skinMIMAG],[Human-skin],[MIMAG]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMisag.md b/mixs6/Human-skinMisag.md new file mode 100644 index 00000000..e49a32cf --- /dev/null +++ b/mixs6/Human-skinMisag.md @@ -0,0 +1,455 @@ + +# Class: Human-skinMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-skin + +URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-skin]^-[Human-skinMISAG],[Human-skin],[MISAG]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMiuvig.md b/mixs6/Human-skinMiuvig.md new file mode 100644 index 00000000..c0b07e9c --- /dev/null +++ b/mixs6/Human-skinMiuvig.md @@ -0,0 +1,525 @@ + +# Class: Human-skinMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIUVIG](https://w3id.org/mixs/vocab/Human-skinMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-skin]^-[Human-skinMIUVIG],[Human-skin],[MIUVIG]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginal.md b/mixs6/Human-vaginal.md new file mode 100644 index 00000000..f4a6815c --- /dev/null +++ b/mixs6/Human-vaginal.md @@ -0,0 +1,237 @@ + +# Class: Human-vaginal + + +human-vaginal + +URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIUVIG],[Human-vaginalMISAG],[Human-vaginalMIMARKSSurvey],[Human-vaginalMIMARKSSpecimen],[Human-vaginalMIMAG],[Human-vaginalMIGSVirus],[Human-vaginalMIGSPlant],[Human-vaginalMIGSOrg],[Human-vaginalMIGSEukaryote],[Human-vaginalMIGSBacteria],[Human-vaginalME],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMIGSBacteria.md b/mixs6/Human-vaginalMIGSBacteria.md new file mode 100644 index 00000000..a1c1683c --- /dev/null +++ b/mixs6/Human-vaginalMIGSBacteria.md @@ -0,0 +1,468 @@ + +# Class: Human-vaginalMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-vaginalMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-vaginal]^-[Human-vaginalMIGSBacteria],[Human-vaginal],[MIGSBacteria]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIGSEukaryote.md b/mixs6/Human-vaginalMIGSEukaryote.md new file mode 100644 index 00000000..43feb6c8 --- /dev/null +++ b/mixs6/Human-vaginalMIGSEukaryote.md @@ -0,0 +1,468 @@ + +# Class: Human-vaginalMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-vaginalMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-vaginal]^-[Human-vaginalMIGSEukaryote],[Human-vaginal],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIGSPlant.md b/mixs6/Human-vaginalMIGSPlant.md new file mode 100644 index 00000000..e4e194c1 --- /dev/null +++ b/mixs6/Human-vaginalMIGSPlant.md @@ -0,0 +1,438 @@ + +# Class: Human-vaginalMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vaginalMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-vaginal]^-[Human-vaginalMIGSPlant],[Human-vaginal],[MIGSPlant]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIGSVirus.md b/mixs6/Human-vaginalMIGSVirus.md new file mode 100644 index 00000000..0b7797dd --- /dev/null +++ b/mixs6/Human-vaginalMIGSVirus.md @@ -0,0 +1,463 @@ + +# Class: Human-vaginalMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vaginalMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-vaginal]^-[Human-vaginalMIGSVirus],[Human-vaginal],[MIGSVirus]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-vaginalMIMARKSSpecimen.md b/mixs6/Human-vaginalMIMARKSSpecimen.md new file mode 100644 index 00000000..ec40fba1 --- /dev/null +++ b/mixs6/Human-vaginalMIMARKSSpecimen.md @@ -0,0 +1,388 @@ + +# Class: Human-vaginalMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-vaginalMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-vaginal]^-[Human-vaginalMIMARKSSpecimen],[Human-vaginal],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIMARKSSurvey.md b/mixs6/Human-vaginalMIMARKSSurvey.md new file mode 100644 index 00000000..dcb71676 --- /dev/null +++ b/mixs6/Human-vaginalMIMARKSSurvey.md @@ -0,0 +1,368 @@ + +# Class: Human-vaginalMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-vaginalMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-vaginal]^-[Human-vaginalMIMARKSSurvey],[Human-vaginal],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMe.md b/mixs6/Human-vaginalMe.md new file mode 100644 index 00000000..9223b69e --- /dev/null +++ b/mixs6/Human-vaginalMe.md @@ -0,0 +1,403 @@ + +# Class: Human-vaginalME + + +Combinatorial checklist Metagenome or Environmental with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-vaginal]^-[Human-vaginalME],[Human-vaginal],[ME]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsOrg.md b/mixs6/Human-vaginalMigsOrg.md new file mode 100644 index 00000000..c26c49f9 --- /dev/null +++ b/mixs6/Human-vaginalMigsOrg.md @@ -0,0 +1,423 @@ + +# Class: Human-vaginalMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginalMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-vaginal]^-[Human-vaginalMIGSOrg],[Human-vaginal],[MIGSOrg]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMimag.md b/mixs6/Human-vaginalMimag.md new file mode 100644 index 00000000..f6c9ae6c --- /dev/null +++ b/mixs6/Human-vaginalMimag.md @@ -0,0 +1,478 @@ + +# Class: Human-vaginalMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-vaginal]^-[Human-vaginalMIMAG],[Human-vaginal],[MIMAG]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMisag.md b/mixs6/Human-vaginalMisag.md new file mode 100644 index 00000000..77e4271b --- /dev/null +++ b/mixs6/Human-vaginalMisag.md @@ -0,0 +1,483 @@ + +# Class: Human-vaginalMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-vaginal]^-[Human-vaginalMISAG],[Human-vaginal],[MISAG]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMiuvig.md b/mixs6/Human-vaginalMiuvig.md new file mode 100644 index 00000000..ff8c79b1 --- /dev/null +++ b/mixs6/Human-vaginalMiuvig.md @@ -0,0 +1,553 @@ + +# Class: Human-vaginalMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-vaginal]^-[Human-vaginalMIUVIG],[Human-vaginal],[MIUVIG]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-cores.md b/mixs6/HydrocarbonResources-cores.md new file mode 100644 index 00000000..43d45b7a --- /dev/null +++ b/mixs6/HydrocarbonResources-cores.md @@ -0,0 +1,385 @@ + +# Class: HydrocarbonResources-cores + + +hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/HydrocarbonResources-cores) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIUVIG],[HydrocarbonResources-coresMISAG],[HydrocarbonResources-coresMIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSpecimen],[HydrocarbonResources-coresMIMAG],[HydrocarbonResources-coresMIGSVirus],[HydrocarbonResources-coresMIGSPlant],[HydrocarbonResources-coresMIGSOrg],[HydrocarbonResources-coresMIGSEukaryote],[HydrocarbonResources-coresMIGSBacteria],[HydrocarbonResources-coresME],[QuantityValue]OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMIGSBacteria.md b/mixs6/HydrocarbonResources-coresMIGSBacteria.md new file mode 100644 index 00000000..fab846f1 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIGSBacteria.md @@ -0,0 +1,616 @@ + +# Class: HydrocarbonResources-coresMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSBacteria](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSBacteria],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSBacteria],[HydrocarbonResources-cores],[MIGSBacteria]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIGSEukaryote.md b/mixs6/HydrocarbonResources-coresMIGSEukaryote.md new file mode 100644 index 00000000..d8f04085 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIGSEukaryote.md @@ -0,0 +1,616 @@ + +# Class: HydrocarbonResources-coresMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSEukaryote],[HydrocarbonResources-cores],[MIGSEukaryote]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIGSPlant.md b/mixs6/HydrocarbonResources-coresMIGSPlant.md new file mode 100644 index 00000000..ae26c134 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIGSPlant.md @@ -0,0 +1,586 @@ + +# Class: HydrocarbonResources-coresMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSPlant],[HydrocarbonResources-cores],[MIGSPlant]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIGSVirus.md b/mixs6/HydrocarbonResources-coresMIGSVirus.md new file mode 100644 index 00000000..09190183 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIGSVirus.md @@ -0,0 +1,611 @@ + +# Class: HydrocarbonResources-coresMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSVirus],[HydrocarbonResources-cores],[MIGSVirus]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md b/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md new file mode 100644 index 00000000..f6e3b20a --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md @@ -0,0 +1,536 @@ + +# Class: HydrocarbonResources-coresMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSpecimen],[HydrocarbonResources-cores],[MIMARKSSpecimen]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md b/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md new file mode 100644 index 00000000..a7751730 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md @@ -0,0 +1,516 @@ + +# Class: HydrocarbonResources-coresMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSurvey],[HydrocarbonResources-cores],[MIMARKSSurvey]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMe.md b/mixs6/HydrocarbonResources-coresMe.md new file mode 100644 index 00000000..74ea6ccd --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMe.md @@ -0,0 +1,551 @@ + +# Class: HydrocarbonResources-coresME + + +Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/HydrocarbonResources-coresME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresME],[HydrocarbonResources-cores],[ME]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsOrg.md b/mixs6/HydrocarbonResources-coresMigsOrg.md new file mode 100644 index 00000000..a0389207 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMigsOrg.md @@ -0,0 +1,571 @@ + +# Class: HydrocarbonResources-coresMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSOrg],[HydrocarbonResources-cores],[MIGSOrg]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMimag.md b/mixs6/HydrocarbonResources-coresMimag.md new file mode 100644 index 00000000..c7df31cd --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMimag.md @@ -0,0 +1,626 @@ + +# Class: HydrocarbonResources-coresMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMAG],[HydrocarbonResources-cores],[MIMAG]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMisag.md b/mixs6/HydrocarbonResources-coresMisag.md new file mode 100644 index 00000000..ff32bcce --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMisag.md @@ -0,0 +1,631 @@ + +# Class: HydrocarbonResources-coresMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMISAG],[HydrocarbonResources-cores],[MISAG]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMiuvig.md b/mixs6/HydrocarbonResources-coresMiuvig.md new file mode 100644 index 00000000..4e6e13ce --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMiuvig.md @@ -0,0 +1,701 @@ + +# Class: HydrocarbonResources-coresMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIUVIG],[HydrocarbonResources-cores],[MIUVIG]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabs.md b/mixs6/HydrocarbonResources-fluidsSwabs.md new file mode 100644 index 00000000..3d005358 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabs.md @@ -0,0 +1,405 @@ + +# Class: HydrocarbonResources-fluidsSwabs + + +hydrocarbon resources-fluids/swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabs) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-fluidsSwabsME],[QuantityValue]OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSBacteria.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSBacteria.md new file mode 100644 index 00000000..2904aa2e --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSBacteria.md @@ -0,0 +1,636 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSBacteria],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-fluidsSwabs],[MIGSBacteria]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md new file mode 100644 index 00000000..0ccd0bee --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md @@ -0,0 +1,636 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-fluidsSwabs],[MIGSEukaryote]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md new file mode 100644 index 00000000..65133b69 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md @@ -0,0 +1,606 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-fluidsSwabs],[MIGSPlant]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md new file mode 100644 index 00000000..15275a35 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md @@ -0,0 +1,631 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-fluidsSwabs],[MIGSVirus]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md new file mode 100644 index 00000000..10ecf5f1 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md @@ -0,0 +1,556 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs],[MIMARKSSpecimen]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md new file mode 100644 index 00000000..1d8ebd20 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md @@ -0,0 +1,536 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-fluidsSwabs],[MIMARKSSurvey]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMe.md b/mixs6/HydrocarbonResources-fluidsSwabsMe.md new file mode 100644 index 00000000..3b518363 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMe.md @@ -0,0 +1,571 @@ + +# Class: HydrocarbonResources-fluidsSwabsME + + +Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-fluidsSwabs],[ME]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md new file mode 100644 index 00000000..f58c9d62 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md @@ -0,0 +1,591 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-fluidsSwabs],[MIGSOrg]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md new file mode 100644 index 00000000..2ef0932e --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md @@ -0,0 +1,646 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-fluidsSwabs],[MIMAG]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md new file mode 100644 index 00000000..5f89ef72 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md @@ -0,0 +1,651 @@ + +# Class: HydrocarbonResources-fluidsSwabsMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-fluidsSwabs],[MISAG]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md new file mode 100644 index 00000000..ba00f372 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md @@ -0,0 +1,721 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-fluidsSwabs],[MIUVIG]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [Date](types/Date.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/IndoorSpaceEnum.md b/mixs6/IndoorSpaceEnum.md new file mode 100644 index 00000000..7b26fd99 --- /dev/null +++ b/mixs6/IndoorSpaceEnum.md @@ -0,0 +1,19 @@ + +# Enum: indoor_space_enum + + + + +URI: [mixs.vocab:indoor_space_enum](https://w3id.org/mixs/vocab/indoor_space_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/IndoorSurfEnum.md b/mixs6/IndoorSurfEnum.md new file mode 100644 index 00000000..726d4e28 --- /dev/null +++ b/mixs6/IndoorSurfEnum.md @@ -0,0 +1,19 @@ + +# Enum: indoor_surf_enum + + + + +URI: [mixs.vocab:indoor_surf_enum](https://w3id.org/mixs/vocab/indoor_surf_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/IntWallCondEnum.md b/mixs6/IntWallCondEnum.md new file mode 100644 index 00000000..43294c18 --- /dev/null +++ b/mixs6/IntWallCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: int_wall_cond_enum + + + + +URI: [mixs.vocab:int_wall_cond_enum](https://w3id.org/mixs/vocab/int_wall_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/InvestigationTypeEnum.md b/mixs6/InvestigationTypeEnum.md new file mode 100644 index 00000000..cbb53e4c --- /dev/null +++ b/mixs6/InvestigationTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: investigation_type_enum + + + + +URI: [mixs.vocab:investigation_type_enum](https://w3id.org/mixs/vocab/investigation_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/LibLayoutEnum.md b/mixs6/LibLayoutEnum.md new file mode 100644 index 00000000..f0f31110 --- /dev/null +++ b/mixs6/LibLayoutEnum.md @@ -0,0 +1,19 @@ + +# Enum: lib_layout_enum + + + + +URI: [mixs.vocab:lib_layout_enum](https://w3id.org/mixs/vocab/lib_layout_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/LightTypeEnum.md b/mixs6/LightTypeEnum.md new file mode 100644 index 00000000..82eb06e8 --- /dev/null +++ b/mixs6/LightTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: light_type_enum + + + + +URI: [mixs.vocab:light_type_enum](https://w3id.org/mixs/vocab/light_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/LithologyEnum.md b/mixs6/LithologyEnum.md new file mode 100644 index 00000000..1c2a5288 --- /dev/null +++ b/mixs6/LithologyEnum.md @@ -0,0 +1,19 @@ + +# Enum: lithology_enum + + + + +URI: [mixs.vocab:lithology_enum](https://w3id.org/mixs/vocab/lithology_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ME_sample_collect_device.md b/mixs6/ME_sample_collect_device.md new file mode 100644 index 00000000..8f525232 --- /dev/null +++ b/mixs6/ME_sample_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: ME_sample_collect_device + + + + +URI: [mixs.vocab:ME_sample_collect_device](https://w3id.org/mixs/vocab/ME_sample_collect_device) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/ME_sample_collect_method.md b/mixs6/ME_sample_collect_method.md new file mode 100644 index 00000000..99ff8992 --- /dev/null +++ b/mixs6/ME_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: ME_sample_collect_method + + + + +URI: [mixs.vocab:ME_sample_collect_method](https://w3id.org/mixs/vocab/ME_sample_collect_method) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGSBacteria.md b/mixs6/MIGSBacteria.md new file mode 100644 index 00000000..c3519267 --- /dev/null +++ b/mixs6/MIGSBacteria.md @@ -0,0 +1,154 @@ + +# Class: MIGSBacteria + + +Minimal Information about a Genome Sequence: cultured bacteria/archaea + +URI: [mixs.vocab:MIGSBacteria](https://w3id.org/mixs/vocab/MIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSBacteria],[WastewaterSludgeMIGSBacteria]uses%20-.->[MIGSBacteria],[SoilMIGSBacteria]uses%20-.->[MIGSBacteria],[SedimentMIGSBacteria]uses%20-.->[MIGSBacteria],[Plant-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[MicrobialMatBiofilmMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-coresMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-vaginalMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-skinMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-oralMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-gutMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[Host-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[BuiltEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[AirMIGSBacteria]uses%20-.->[MIGSBacteria],[WaterMIGSBacteria],[WastewaterSludgeMIGSBacteria],[SoilMIGSBacteria],[SedimentMIGSBacteria],[Plant-associatedMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MicrobialMatBiofilmMIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-coresMIGSBacteria],[Human-vaginalMIGSBacteria],[Human-skinMIGSBacteria],[Human-oralMIGSBacteria],[Human-gutMIGSBacteria],[Human-associatedMIGSBacteria],[Host-associatedMIGSBacteria],[BuiltEnvironmentMIGSBacteria],[AirMIGSBacteria]) + +## Mixin for + + * [AirMIGSBacteria](AirMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SoilMIGSBacteria](SoilMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WaterMIGSBacteria](WaterMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + * [MIGS bacteria➞collection_date](MIGS_bacteria_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞env_broad_scale](MIGS_bacteria_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞env_local_scale](MIGS_bacteria_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞env_medium](MIGS_bacteria_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞geo_loc_name](MIGS_bacteria_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞lat_lon](MIGS_bacteria_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.ba | + diff --git a/mixs6/MIGSEukaryote.md b/mixs6/MIGSEukaryote.md new file mode 100644 index 00000000..2f820aa2 --- /dev/null +++ b/mixs6/MIGSEukaryote.md @@ -0,0 +1,154 @@ + +# Class: MIGSEukaryote + + +Minimal Information about a Genome Sequence: eukaryote + +URI: [mixs.vocab:MIGSEukaryote](https://w3id.org/mixs/vocab/MIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSEukaryote],[WastewaterSludgeMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SoilMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SedimentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Plant-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-vaginalMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-skinMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-oralMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-gutMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Host-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[BuiltEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[AirMIGSEukaryote]uses%20-.->[MIGSEukaryote],[WaterMIGSEukaryote],[WastewaterSludgeMIGSEukaryote],[SoilMIGSEukaryote],[SedimentMIGSEukaryote],[Plant-associatedMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote],[Human-vaginalMIGSEukaryote],[Human-skinMIGSEukaryote],[Human-oralMIGSEukaryote],[Human-gutMIGSEukaryote],[Human-associatedMIGSEukaryote],[Host-associatedMIGSEukaryote],[BuiltEnvironmentMIGSEukaryote],[AirMIGSEukaryote]) + +## Mixin for + + * [AirMIGSEukaryote](AirMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package air + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package built environment + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package host-associated + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-associated + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-gut + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-oral + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-skin + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package plant-associated + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package sediment + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package soil + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package wastewater_sludge + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + * [MIGS eukaryote➞collection_date](MIGS_eukaryote_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞env_broad_scale](MIGS_eukaryote_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞env_local_scale](MIGS_eukaryote_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞env_medium](MIGS_eukaryote_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞geo_loc_name](MIGS_eukaryote_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞lat_lon](MIGS_eukaryote_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.eu | + diff --git a/mixs6/MIGSPlant.md b/mixs6/MIGSPlant.md new file mode 100644 index 00000000..ed32693e --- /dev/null +++ b/mixs6/MIGSPlant.md @@ -0,0 +1,142 @@ + +# Class: MIGSPlant + + +Minimal Information about a Genome Sequence: plant + +URI: [mixs.vocab:MIGSPlant](https://w3id.org/mixs/vocab/MIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSPlant],[WastewaterSludgeMIGSPlant]uses%20-.->[MIGSPlant],[SoilMIGSPlant]uses%20-.->[MIGSPlant],[SedimentMIGSPlant]uses%20-.->[MIGSPlant],[Plant-associatedMIGSPlant]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[MicrobialMatBiofilmMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-coresMIGSPlant]uses%20-.->[MIGSPlant],[Human-vaginalMIGSPlant]uses%20-.->[MIGSPlant],[Human-skinMIGSPlant]uses%20-.->[MIGSPlant],[Human-oralMIGSPlant]uses%20-.->[MIGSPlant],[Human-gutMIGSPlant]uses%20-.->[MIGSPlant],[Human-associatedMIGSPlant]uses%20-.->[MIGSPlant],[Host-associatedMIGSPlant]uses%20-.->[MIGSPlant],[BuiltEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[AirMIGSPlant]uses%20-.->[MIGSPlant],[WaterMIGSPlant],[WastewaterSludgeMIGSPlant],[SoilMIGSPlant],[SedimentMIGSPlant],[Plant-associatedMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MicrobialMatBiofilmMIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-coresMIGSPlant],[Human-vaginalMIGSPlant],[Human-skinMIGSPlant],[Human-oralMIGSPlant],[Human-gutMIGSPlant],[Human-associatedMIGSPlant],[Host-associatedMIGSPlant],[BuiltEnvironmentMIGSPlant],[AirMIGSPlant]) + +## Mixin for + + * [AirMIGSPlant](AirMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package air + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package built environment + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package host-associated + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-associated + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-gut + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-oral + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-skin + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package plant-associated + * [SedimentMIGSPlant](SedimentMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package sediment + * [SoilMIGSPlant](SoilMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package soil + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package wastewater_sludge + * [WaterMIGSPlant](WaterMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞collection_date](MIGS_plant_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞env_broad_scale](MIGS_plant_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞env_local_scale](MIGS_plant_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞env_medium](MIGS_plant_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞geo_loc_name](MIGS_plant_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞lat_lon](MIGS_plant_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.pl | + diff --git a/mixs6/MIGSVirus.md b/mixs6/MIGSVirus.md new file mode 100644 index 00000000..7513e059 --- /dev/null +++ b/mixs6/MIGSVirus.md @@ -0,0 +1,152 @@ + +# Class: MIGSVirus + + +Minimal Information about a Genome Sequence: cultured bacteria/archaea + +URI: [mixs.vocab:MIGSVirus](https://w3id.org/mixs/vocab/MIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSVirus],[WastewaterSludgeMIGSVirus]uses%20-.->[MIGSVirus],[SoilMIGSVirus]uses%20-.->[MIGSVirus],[SedimentMIGSVirus]uses%20-.->[MIGSVirus],[Plant-associatedMIGSVirus]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[MicrobialMatBiofilmMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-coresMIGSVirus]uses%20-.->[MIGSVirus],[Human-vaginalMIGSVirus]uses%20-.->[MIGSVirus],[Human-skinMIGSVirus]uses%20-.->[MIGSVirus],[Human-oralMIGSVirus]uses%20-.->[MIGSVirus],[Human-gutMIGSVirus]uses%20-.->[MIGSVirus],[Human-associatedMIGSVirus]uses%20-.->[MIGSVirus],[Host-associatedMIGSVirus]uses%20-.->[MIGSVirus],[BuiltEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[AirMIGSVirus]uses%20-.->[MIGSVirus],[WaterMIGSVirus],[WastewaterSludgeMIGSVirus],[SoilMIGSVirus],[SedimentMIGSVirus],[Plant-associatedMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MicrobialMatBiofilmMIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-coresMIGSVirus],[Human-vaginalMIGSVirus],[Human-skinMIGSVirus],[Human-oralMIGSVirus],[Human-gutMIGSVirus],[Human-associatedMIGSVirus],[Host-associatedMIGSVirus],[BuiltEnvironmentMIGSVirus],[AirMIGSVirus]) + +## Mixin for + + * [AirMIGSVirus](AirMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [SedimentMIGSVirus](SedimentMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SoilMIGSVirus](SoilMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WaterMIGSVirus](WaterMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + * [MIGS virus➞collection_date](MIGS_virus_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞env_broad_scale](MIGS_virus_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞env_local_scale](MIGS_virus_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞env_medium](MIGS_virus_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞geo_loc_name](MIGS_virus_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞lat_lon](MIGS_virus_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.ba | + diff --git a/mixs6/MIGS_bacteria_adapters.md b/mixs6/MIGS_bacteria_adapters.md new file mode 100644 index 00000000..530ada43 --- /dev/null +++ b/mixs6/MIGS_bacteria_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_adapters + + + + +URI: [mixs.vocab:MIGS_bacteria_adapters](https://w3id.org/mixs/vocab/MIGS_bacteria_adapters) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_annot.md b/mixs6/MIGS_bacteria_annot.md new file mode 100644 index 00000000..ba2250ae --- /dev/null +++ b/mixs6/MIGS_bacteria_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_annot + + + + +URI: [mixs.vocab:MIGS_bacteria_annot](https://w3id.org/mixs/vocab/MIGS_bacteria_annot) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_assembly_name.md b/mixs6/MIGS_bacteria_assembly_name.md new file mode 100644 index 00000000..4840fe88 --- /dev/null +++ b/mixs6/MIGS_bacteria_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_assembly_name + + + + +URI: [mixs.vocab:MIGS_bacteria_assembly_name](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_assembly_qual.md b/mixs6/MIGS_bacteria_assembly_qual.md new file mode 100644 index 00000000..ca60c110 --- /dev/null +++ b/mixs6/MIGS_bacteria_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_assembly_qual + + + + +URI: [mixs.vocab:MIGS_bacteria_assembly_qual](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_qual) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_assembly_software.md b/mixs6/MIGS_bacteria_assembly_software.md new file mode 100644 index 00000000..a3929cfd --- /dev/null +++ b/mixs6/MIGS_bacteria_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_assembly_software + + + + +URI: [mixs.vocab:MIGS_bacteria_assembly_software](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_software) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_biotic_relationship.md b/mixs6/MIGS_bacteria_biotic_relationship.md new file mode 100644 index 00000000..b93d07c6 --- /dev/null +++ b/mixs6/MIGS_bacteria_biotic_relationship.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_biotic_relationship + + + + +URI: [mixs.vocab:MIGS_bacteria_biotic_relationship](https://w3id.org/mixs/vocab/MIGS_bacteria_biotic_relationship) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_collection_date.md b/mixs6/MIGS_bacteria_collection_date.md new file mode 100644 index 00000000..bb003eaf --- /dev/null +++ b/mixs6/MIGS_bacteria_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_collection_date + + + + +URI: [mixs.vocab:MIGS_bacteria_collection_date](https://w3id.org/mixs/vocab/MIGS_bacteria_collection_date) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_compl_score.md b/mixs6/MIGS_bacteria_compl_score.md new file mode 100644 index 00000000..e7449551 --- /dev/null +++ b/mixs6/MIGS_bacteria_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_compl_score + + + + +URI: [mixs.vocab:MIGS_bacteria_compl_score](https://w3id.org/mixs/vocab/MIGS_bacteria_compl_score) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_compl_software.md b/mixs6/MIGS_bacteria_compl_software.md new file mode 100644 index 00000000..30a096ec --- /dev/null +++ b/mixs6/MIGS_bacteria_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_compl_software + + + + +URI: [mixs.vocab:MIGS_bacteria_compl_software](https://w3id.org/mixs/vocab/MIGS_bacteria_compl_software) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_encoded_traits.md b/mixs6/MIGS_bacteria_encoded_traits.md new file mode 100644 index 00000000..6f2c8cef --- /dev/null +++ b/mixs6/MIGS_bacteria_encoded_traits.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_encoded_traits + + + + +URI: [mixs.vocab:MIGS_bacteria_encoded_traits](https://w3id.org/mixs/vocab/MIGS_bacteria_encoded_traits) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_broad_scale.md b/mixs6/MIGS_bacteria_env_broad_scale.md new file mode 100644 index 00000000..f1d226fb --- /dev/null +++ b/mixs6/MIGS_bacteria_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_bacteria_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_bacteria_env_broad_scale) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_local_scale.md b/mixs6/MIGS_bacteria_env_local_scale.md new file mode 100644 index 00000000..f1b4fbcf --- /dev/null +++ b/mixs6/MIGS_bacteria_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_env_local_scale + + + + +URI: [mixs.vocab:MIGS_bacteria_env_local_scale](https://w3id.org/mixs/vocab/MIGS_bacteria_env_local_scale) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_medium.md b/mixs6/MIGS_bacteria_env_medium.md new file mode 100644 index 00000000..ed3db8c9 --- /dev/null +++ b/mixs6/MIGS_bacteria_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_env_medium + + + + +URI: [mixs.vocab:MIGS_bacteria_env_medium](https://w3id.org/mixs/vocab/MIGS_bacteria_env_medium) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_package.md b/mixs6/MIGS_bacteria_env_package.md new file mode 100644 index 00000000..20b75103 --- /dev/null +++ b/mixs6/MIGS_bacteria_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_env_package + + + + +URI: [mixs.vocab:MIGS_bacteria_env_package](https://w3id.org/mixs/vocab/MIGS_bacteria_env_package) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_estimated_size.md b/mixs6/MIGS_bacteria_estimated_size.md new file mode 100644 index 00000000..7eb1f474 --- /dev/null +++ b/mixs6/MIGS_bacteria_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_estimated_size + + + + +URI: [mixs.vocab:MIGS_bacteria_estimated_size](https://w3id.org/mixs/vocab/MIGS_bacteria_estimated_size) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_experimental_factor.md b/mixs6/MIGS_bacteria_experimental_factor.md new file mode 100644 index 00000000..6ba4686f --- /dev/null +++ b/mixs6/MIGS_bacteria_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_experimental_factor + + + + +URI: [mixs.vocab:MIGS_bacteria_experimental_factor](https://w3id.org/mixs/vocab/MIGS_bacteria_experimental_factor) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_extrachrom_elements.md b/mixs6/MIGS_bacteria_extrachrom_elements.md new file mode 100644 index 00000000..f2b616c5 --- /dev/null +++ b/mixs6/MIGS_bacteria_extrachrom_elements.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_extrachrom_elements + + + + +URI: [mixs.vocab:MIGS_bacteria_extrachrom_elements](https://w3id.org/mixs/vocab/MIGS_bacteria_extrachrom_elements) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_feat_pred.md b/mixs6/MIGS_bacteria_feat_pred.md new file mode 100644 index 00000000..e68bea98 --- /dev/null +++ b/mixs6/MIGS_bacteria_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_feat_pred + + + + +URI: [mixs.vocab:MIGS_bacteria_feat_pred](https://w3id.org/mixs/vocab/MIGS_bacteria_feat_pred) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_geo_loc_name.md b/mixs6/MIGS_bacteria_geo_loc_name.md new file mode 100644 index 00000000..12b29dc6 --- /dev/null +++ b/mixs6/MIGS_bacteria_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_bacteria_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_bacteria_geo_loc_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_health_disease_stat.md b/mixs6/MIGS_bacteria_health_disease_stat.md new file mode 100644 index 00000000..050830a8 --- /dev/null +++ b/mixs6/MIGS_bacteria_health_disease_stat.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_health_disease_stat + + + + +URI: [mixs.vocab:MIGS_bacteria_health_disease_stat](https://w3id.org/mixs/vocab/MIGS_bacteria_health_disease_stat) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_host_spec_range.md b/mixs6/MIGS_bacteria_host_spec_range.md new file mode 100644 index 00000000..01e1272c --- /dev/null +++ b/mixs6/MIGS_bacteria_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_host_spec_range + + + + +URI: [mixs.vocab:MIGS_bacteria_host_spec_range](https://w3id.org/mixs/vocab/MIGS_bacteria_host_spec_range) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_investigation_type.md b/mixs6/MIGS_bacteria_investigation_type.md new file mode 100644 index 00000000..f1778d90 --- /dev/null +++ b/mixs6/MIGS_bacteria_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_investigation_type + + + + +URI: [mixs.vocab:MIGS_bacteria_investigation_type](https://w3id.org/mixs/vocab/MIGS_bacteria_investigation_type) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_isol_growth_condt.md b/mixs6/MIGS_bacteria_isol_growth_condt.md new file mode 100644 index 00000000..a8b860f4 --- /dev/null +++ b/mixs6/MIGS_bacteria_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_bacteria_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_bacteria_isol_growth_condt) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lat_lon.md b/mixs6/MIGS_bacteria_lat_lon.md new file mode 100644 index 00000000..0a32974d --- /dev/null +++ b/mixs6/MIGS_bacteria_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_lat_lon + + + + +URI: [mixs.vocab:MIGS_bacteria_lat_lon](https://w3id.org/mixs/vocab/MIGS_bacteria_lat_lon) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_layout.md b/mixs6/MIGS_bacteria_lib_layout.md new file mode 100644 index 00000000..44eaa376 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_layout + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_layout](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_layout) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_reads_seqd.md b/mixs6/MIGS_bacteria_lib_reads_seqd.md new file mode 100644 index 00000000..dbb90ba1 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_reads_seqd) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_screen.md b/mixs6/MIGS_bacteria_lib_screen.md new file mode 100644 index 00000000..3cb6fb63 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_screen + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_screen](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_screen) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_size.md b/mixs6/MIGS_bacteria_lib_size.md new file mode 100644 index 00000000..a4cc3d07 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_size + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_size](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_size) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_vector.md b/mixs6/MIGS_bacteria_lib_vector.md new file mode 100644 index 00000000..3ef72937 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_vector + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_vector](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_vector) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_nucl_acid_amp.md b/mixs6/MIGS_bacteria_nucl_acid_amp.md new file mode 100644 index 00000000..f14fab06 --- /dev/null +++ b/mixs6/MIGS_bacteria_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_bacteria_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_bacteria_nucl_acid_amp) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_nucl_acid_ext.md b/mixs6/MIGS_bacteria_nucl_acid_ext.md new file mode 100644 index 00000000..989e74d3 --- /dev/null +++ b/mixs6/MIGS_bacteria_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_bacteria_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_bacteria_nucl_acid_ext) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_num_replicons.md b/mixs6/MIGS_bacteria_num_replicons.md new file mode 100644 index 00000000..86077b1b --- /dev/null +++ b/mixs6/MIGS_bacteria_num_replicons.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_num_replicons + + + + +URI: [mixs.vocab:MIGS_bacteria_num_replicons](https://w3id.org/mixs/vocab/MIGS_bacteria_num_replicons) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_number_contig.md b/mixs6/MIGS_bacteria_number_contig.md new file mode 100644 index 00000000..ffdcfccb --- /dev/null +++ b/mixs6/MIGS_bacteria_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_number_contig + + + + +URI: [mixs.vocab:MIGS_bacteria_number_contig](https://w3id.org/mixs/vocab/MIGS_bacteria_number_contig) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_pathogenicity.md b/mixs6/MIGS_bacteria_pathogenicity.md new file mode 100644 index 00000000..2448a700 --- /dev/null +++ b/mixs6/MIGS_bacteria_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_pathogenicity + + + + +URI: [mixs.vocab:MIGS_bacteria_pathogenicity](https://w3id.org/mixs/vocab/MIGS_bacteria_pathogenicity) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_project_name.md b/mixs6/MIGS_bacteria_project_name.md new file mode 100644 index 00000000..851f2d86 --- /dev/null +++ b/mixs6/MIGS_bacteria_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_project_name + + + + +URI: [mixs.vocab:MIGS_bacteria_project_name](https://w3id.org/mixs/vocab/MIGS_bacteria_project_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_ref_biomaterial.md b/mixs6/MIGS_bacteria_ref_biomaterial.md new file mode 100644 index 00000000..06813701 --- /dev/null +++ b/mixs6/MIGS_bacteria_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_bacteria_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_bacteria_ref_biomaterial) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_ref_db.md b/mixs6/MIGS_bacteria_ref_db.md new file mode 100644 index 00000000..d9f9d9c4 --- /dev/null +++ b/mixs6/MIGS_bacteria_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_ref_db + + + + +URI: [mixs.vocab:MIGS_bacteria_ref_db](https://w3id.org/mixs/vocab/MIGS_bacteria_ref_db) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_rel_to_oxygen.md b/mixs6/MIGS_bacteria_rel_to_oxygen.md new file mode 100644 index 00000000..17434d02 --- /dev/null +++ b/mixs6/MIGS_bacteria_rel_to_oxygen.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_rel_to_oxygen + + + + +URI: [mixs.vocab:MIGS_bacteria_rel_to_oxygen](https://w3id.org/mixs/vocab/MIGS_bacteria_rel_to_oxygen) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_samp_mat_process.md b/mixs6/MIGS_bacteria_samp_mat_process.md new file mode 100644 index 00000000..2f443358 --- /dev/null +++ b/mixs6/MIGS_bacteria_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_bacteria_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_bacteria_samp_mat_process) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_samp_size.md b/mixs6/MIGS_bacteria_samp_size.md new file mode 100644 index 00000000..bf67e5c2 --- /dev/null +++ b/mixs6/MIGS_bacteria_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_samp_size + + + + +URI: [mixs.vocab:MIGS_bacteria_samp_size](https://w3id.org/mixs/vocab/MIGS_bacteria_samp_size) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sample_collect_device.md b/mixs6/MIGS_bacteria_sample_collect_device.md new file mode 100644 index 00000000..c87d7b80 --- /dev/null +++ b/mixs6/MIGS_bacteria_sample_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_sample_collect_device + + + + +URI: [mixs.vocab:MIGS_bacteria_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_bacteria_sample_collect_device) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sample_collect_method.md b/mixs6/MIGS_bacteria_sample_collect_method.md new file mode 100644 index 00000000..1eaee283 --- /dev/null +++ b/mixs6/MIGS_bacteria_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_bacteria_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_bacteria_sample_collect_method) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sample_name.md b/mixs6/MIGS_bacteria_sample_name.md new file mode 100644 index 00000000..59b30f9e --- /dev/null +++ b/mixs6/MIGS_bacteria_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_sample_name + + + + +URI: [mixs.vocab:MIGS_bacteria_sample_name](https://w3id.org/mixs/vocab/MIGS_bacteria_sample_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_seq_meth.md b/mixs6/MIGS_bacteria_seq_meth.md new file mode 100644 index 00000000..7c6dac2d --- /dev/null +++ b/mixs6/MIGS_bacteria_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_seq_meth + + + + +URI: [mixs.vocab:MIGS_bacteria_seq_meth](https://w3id.org/mixs/vocab/MIGS_bacteria_seq_meth) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sim_search_meth.md b/mixs6/MIGS_bacteria_sim_search_meth.md new file mode 100644 index 00000000..df0061d6 --- /dev/null +++ b/mixs6/MIGS_bacteria_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_bacteria_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_bacteria_sim_search_meth) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sop.md b/mixs6/MIGS_bacteria_sop.md new file mode 100644 index 00000000..30544a2c --- /dev/null +++ b/mixs6/MIGS_bacteria_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_sop + + + + +URI: [mixs.vocab:MIGS_bacteria_sop](https://w3id.org/mixs/vocab/MIGS_bacteria_sop) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_source_mat_id.md b/mixs6/MIGS_bacteria_source_mat_id.md new file mode 100644 index 00000000..f327f648 --- /dev/null +++ b/mixs6/MIGS_bacteria_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_source_mat_id + + + + +URI: [mixs.vocab:MIGS_bacteria_source_mat_id](https://w3id.org/mixs/vocab/MIGS_bacteria_source_mat_id) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_specific_host.md b/mixs6/MIGS_bacteria_specific_host.md new file mode 100644 index 00000000..53a9def4 --- /dev/null +++ b/mixs6/MIGS_bacteria_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_specific_host + + + + +URI: [mixs.vocab:MIGS_bacteria_specific_host](https://w3id.org/mixs/vocab/MIGS_bacteria_specific_host) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_submitted_to_insdc.md b/mixs6/MIGS_bacteria_submitted_to_insdc.md new file mode 100644 index 00000000..43216416 --- /dev/null +++ b/mixs6/MIGS_bacteria_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_bacteria_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_bacteria_submitted_to_insdc) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_subspecf_gen_lin.md b/mixs6/MIGS_bacteria_subspecf_gen_lin.md new file mode 100644 index 00000000..a8a8397c --- /dev/null +++ b/mixs6/MIGS_bacteria_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_bacteria_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_bacteria_subspecf_gen_lin) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_tax_class.md b/mixs6/MIGS_bacteria_tax_class.md new file mode 100644 index 00000000..21493ae4 --- /dev/null +++ b/mixs6/MIGS_bacteria_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_tax_class + + + + +URI: [mixs.vocab:MIGS_bacteria_tax_class](https://w3id.org/mixs/vocab/MIGS_bacteria_tax_class) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_tax_ident.md b/mixs6/MIGS_bacteria_tax_ident.md new file mode 100644 index 00000000..b3b5da8f --- /dev/null +++ b/mixs6/MIGS_bacteria_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_tax_ident + + + + +URI: [mixs.vocab:MIGS_bacteria_tax_ident](https://w3id.org/mixs/vocab/MIGS_bacteria_tax_ident) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_trophic_level.md b/mixs6/MIGS_bacteria_trophic_level.md new file mode 100644 index 00000000..9c41c1ea --- /dev/null +++ b/mixs6/MIGS_bacteria_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_trophic_level + + + + +URI: [mixs.vocab:MIGS_bacteria_trophic_level](https://w3id.org/mixs/vocab/MIGS_bacteria_trophic_level) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_url.md b/mixs6/MIGS_bacteria_url.md new file mode 100644 index 00000000..139e1745 --- /dev/null +++ b/mixs6/MIGS_bacteria_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_url + + + + +URI: [mixs.vocab:MIGS_bacteria_url](https://w3id.org/mixs/vocab/MIGS_bacteria_url) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_adapters.md b/mixs6/MIGS_eukaryote_adapters.md new file mode 100644 index 00000000..eb7a03b6 --- /dev/null +++ b/mixs6/MIGS_eukaryote_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_adapters + + + + +URI: [mixs.vocab:MIGS_eukaryote_adapters](https://w3id.org/mixs/vocab/MIGS_eukaryote_adapters) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_annot.md b/mixs6/MIGS_eukaryote_annot.md new file mode 100644 index 00000000..4e4c0c3c --- /dev/null +++ b/mixs6/MIGS_eukaryote_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_annot + + + + +URI: [mixs.vocab:MIGS_eukaryote_annot](https://w3id.org/mixs/vocab/MIGS_eukaryote_annot) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_assembly_name.md b/mixs6/MIGS_eukaryote_assembly_name.md new file mode 100644 index 00000000..ca703149 --- /dev/null +++ b/mixs6/MIGS_eukaryote_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_assembly_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_assembly_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_assembly_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_assembly_qual.md b/mixs6/MIGS_eukaryote_assembly_qual.md new file mode 100644 index 00000000..5457dd91 --- /dev/null +++ b/mixs6/MIGS_eukaryote_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_assembly_qual + + + + +URI: [mixs.vocab:MIGS_eukaryote_assembly_qual](https://w3id.org/mixs/vocab/MIGS_eukaryote_assembly_qual) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_assembly_software.md b/mixs6/MIGS_eukaryote_assembly_software.md new file mode 100644 index 00000000..d8dd4870 --- /dev/null +++ b/mixs6/MIGS_eukaryote_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_assembly_software + + + + +URI: [mixs.vocab:MIGS_eukaryote_assembly_software](https://w3id.org/mixs/vocab/MIGS_eukaryote_assembly_software) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_biotic_relationship.md b/mixs6/MIGS_eukaryote_biotic_relationship.md new file mode 100644 index 00000000..84b9eb08 --- /dev/null +++ b/mixs6/MIGS_eukaryote_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_biotic_relationship + + + + +URI: [mixs.vocab:MIGS_eukaryote_biotic_relationship](https://w3id.org/mixs/vocab/MIGS_eukaryote_biotic_relationship) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_collection_date.md b/mixs6/MIGS_eukaryote_collection_date.md new file mode 100644 index 00000000..7c0b4e08 --- /dev/null +++ b/mixs6/MIGS_eukaryote_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_collection_date + + + + +URI: [mixs.vocab:MIGS_eukaryote_collection_date](https://w3id.org/mixs/vocab/MIGS_eukaryote_collection_date) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_compl_score.md b/mixs6/MIGS_eukaryote_compl_score.md new file mode 100644 index 00000000..837de7d1 --- /dev/null +++ b/mixs6/MIGS_eukaryote_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_compl_score + + + + +URI: [mixs.vocab:MIGS_eukaryote_compl_score](https://w3id.org/mixs/vocab/MIGS_eukaryote_compl_score) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_compl_software.md b/mixs6/MIGS_eukaryote_compl_software.md new file mode 100644 index 00000000..a0d5e8e6 --- /dev/null +++ b/mixs6/MIGS_eukaryote_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_compl_software + + + + +URI: [mixs.vocab:MIGS_eukaryote_compl_software](https://w3id.org/mixs/vocab/MIGS_eukaryote_compl_software) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_broad_scale.md b/mixs6/MIGS_eukaryote_env_broad_scale.md new file mode 100644 index 00000000..06026e2f --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_broad_scale) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_local_scale.md b/mixs6/MIGS_eukaryote_env_local_scale.md new file mode 100644 index 00000000..00638ff7 --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_env_local_scale + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_local_scale](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_local_scale) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_medium.md b/mixs6/MIGS_eukaryote_env_medium.md new file mode 100644 index 00000000..44572961 --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_env_medium + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_medium](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_medium) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_package.md b/mixs6/MIGS_eukaryote_env_package.md new file mode 100644 index 00000000..ca40b85c --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_env_package + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_package](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_package) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_estimated_size.md b/mixs6/MIGS_eukaryote_estimated_size.md new file mode 100644 index 00000000..815d5701 --- /dev/null +++ b/mixs6/MIGS_eukaryote_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_estimated_size + + + + +URI: [mixs.vocab:MIGS_eukaryote_estimated_size](https://w3id.org/mixs/vocab/MIGS_eukaryote_estimated_size) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_experimental_factor.md b/mixs6/MIGS_eukaryote_experimental_factor.md new file mode 100644 index 00000000..7fb090b6 --- /dev/null +++ b/mixs6/MIGS_eukaryote_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_experimental_factor + + + + +URI: [mixs.vocab:MIGS_eukaryote_experimental_factor](https://w3id.org/mixs/vocab/MIGS_eukaryote_experimental_factor) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_extrachrom_elements.md b/mixs6/MIGS_eukaryote_extrachrom_elements.md new file mode 100644 index 00000000..f40ede50 --- /dev/null +++ b/mixs6/MIGS_eukaryote_extrachrom_elements.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_extrachrom_elements + + + + +URI: [mixs.vocab:MIGS_eukaryote_extrachrom_elements](https://w3id.org/mixs/vocab/MIGS_eukaryote_extrachrom_elements) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_feat_pred.md b/mixs6/MIGS_eukaryote_feat_pred.md new file mode 100644 index 00000000..5dfaf9ea --- /dev/null +++ b/mixs6/MIGS_eukaryote_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_feat_pred + + + + +URI: [mixs.vocab:MIGS_eukaryote_feat_pred](https://w3id.org/mixs/vocab/MIGS_eukaryote_feat_pred) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_geo_loc_name.md b/mixs6/MIGS_eukaryote_geo_loc_name.md new file mode 100644 index 00000000..5f31bb2f --- /dev/null +++ b/mixs6/MIGS_eukaryote_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_geo_loc_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_health_disease_stat.md b/mixs6/MIGS_eukaryote_health_disease_stat.md new file mode 100644 index 00000000..24329f53 --- /dev/null +++ b/mixs6/MIGS_eukaryote_health_disease_stat.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_health_disease_stat + + + + +URI: [mixs.vocab:MIGS_eukaryote_health_disease_stat](https://w3id.org/mixs/vocab/MIGS_eukaryote_health_disease_stat) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_host_spec_range.md b/mixs6/MIGS_eukaryote_host_spec_range.md new file mode 100644 index 00000000..8d6780e2 --- /dev/null +++ b/mixs6/MIGS_eukaryote_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_host_spec_range + + + + +URI: [mixs.vocab:MIGS_eukaryote_host_spec_range](https://w3id.org/mixs/vocab/MIGS_eukaryote_host_spec_range) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_investigation_type.md b/mixs6/MIGS_eukaryote_investigation_type.md new file mode 100644 index 00000000..29dea620 --- /dev/null +++ b/mixs6/MIGS_eukaryote_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_investigation_type + + + + +URI: [mixs.vocab:MIGS_eukaryote_investigation_type](https://w3id.org/mixs/vocab/MIGS_eukaryote_investigation_type) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_isol_growth_condt.md b/mixs6/MIGS_eukaryote_isol_growth_condt.md new file mode 100644 index 00000000..dfe519a3 --- /dev/null +++ b/mixs6/MIGS_eukaryote_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_eukaryote_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_eukaryote_isol_growth_condt) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lat_lon.md b/mixs6/MIGS_eukaryote_lat_lon.md new file mode 100644 index 00000000..f583d145 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_lat_lon + + + + +URI: [mixs.vocab:MIGS_eukaryote_lat_lon](https://w3id.org/mixs/vocab/MIGS_eukaryote_lat_lon) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_layout.md b/mixs6/MIGS_eukaryote_lib_layout.md new file mode 100644 index 00000000..f9a7a1ac --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_layout + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_layout](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_layout) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_reads_seqd.md b/mixs6/MIGS_eukaryote_lib_reads_seqd.md new file mode 100644 index 00000000..a3941435 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_reads_seqd) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_screen.md b/mixs6/MIGS_eukaryote_lib_screen.md new file mode 100644 index 00000000..a142cbc0 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_screen + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_screen](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_screen) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_size.md b/mixs6/MIGS_eukaryote_lib_size.md new file mode 100644 index 00000000..4ca7b8a2 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_size + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_size](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_size) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_vector.md b/mixs6/MIGS_eukaryote_lib_vector.md new file mode 100644 index 00000000..b686f06d --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_vector + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_vector](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_vector) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_nucl_acid_amp.md b/mixs6/MIGS_eukaryote_nucl_acid_amp.md new file mode 100644 index 00000000..13f5f670 --- /dev/null +++ b/mixs6/MIGS_eukaryote_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_eukaryote_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_eukaryote_nucl_acid_amp) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_nucl_acid_ext.md b/mixs6/MIGS_eukaryote_nucl_acid_ext.md new file mode 100644 index 00000000..4c34e35d --- /dev/null +++ b/mixs6/MIGS_eukaryote_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_eukaryote_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_eukaryote_nucl_acid_ext) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_num_replicons.md b/mixs6/MIGS_eukaryote_num_replicons.md new file mode 100644 index 00000000..ca4149ed --- /dev/null +++ b/mixs6/MIGS_eukaryote_num_replicons.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_num_replicons + + + + +URI: [mixs.vocab:MIGS_eukaryote_num_replicons](https://w3id.org/mixs/vocab/MIGS_eukaryote_num_replicons) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_number_contig.md b/mixs6/MIGS_eukaryote_number_contig.md new file mode 100644 index 00000000..30721565 --- /dev/null +++ b/mixs6/MIGS_eukaryote_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_number_contig + + + + +URI: [mixs.vocab:MIGS_eukaryote_number_contig](https://w3id.org/mixs/vocab/MIGS_eukaryote_number_contig) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_pathogenicity.md b/mixs6/MIGS_eukaryote_pathogenicity.md new file mode 100644 index 00000000..df21c4e5 --- /dev/null +++ b/mixs6/MIGS_eukaryote_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_pathogenicity + + + + +URI: [mixs.vocab:MIGS_eukaryote_pathogenicity](https://w3id.org/mixs/vocab/MIGS_eukaryote_pathogenicity) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_ploidy.md b/mixs6/MIGS_eukaryote_ploidy.md new file mode 100644 index 00000000..bc4f92f7 --- /dev/null +++ b/mixs6/MIGS_eukaryote_ploidy.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_ploidy + + + + +URI: [mixs.vocab:MIGS_eukaryote_ploidy](https://w3id.org/mixs/vocab/MIGS_eukaryote_ploidy) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ploidy](ploidy.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_project_name.md b/mixs6/MIGS_eukaryote_project_name.md new file mode 100644 index 00000000..b9b44f2e --- /dev/null +++ b/mixs6/MIGS_eukaryote_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_project_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_project_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_project_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_propagation.md b/mixs6/MIGS_eukaryote_propagation.md new file mode 100644 index 00000000..df273139 --- /dev/null +++ b/mixs6/MIGS_eukaryote_propagation.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_propagation + + + + +URI: [mixs.vocab:MIGS_eukaryote_propagation](https://w3id.org/mixs/vocab/MIGS_eukaryote_propagation) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_ref_biomaterial.md b/mixs6/MIGS_eukaryote_ref_biomaterial.md new file mode 100644 index 00000000..dedde21b --- /dev/null +++ b/mixs6/MIGS_eukaryote_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_eukaryote_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_eukaryote_ref_biomaterial) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_ref_db.md b/mixs6/MIGS_eukaryote_ref_db.md new file mode 100644 index 00000000..9759e30b --- /dev/null +++ b/mixs6/MIGS_eukaryote_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_ref_db + + + + +URI: [mixs.vocab:MIGS_eukaryote_ref_db](https://w3id.org/mixs/vocab/MIGS_eukaryote_ref_db) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_samp_mat_process.md b/mixs6/MIGS_eukaryote_samp_mat_process.md new file mode 100644 index 00000000..e920d891 --- /dev/null +++ b/mixs6/MIGS_eukaryote_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_eukaryote_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_eukaryote_samp_mat_process) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_samp_size.md b/mixs6/MIGS_eukaryote_samp_size.md new file mode 100644 index 00000000..d542b487 --- /dev/null +++ b/mixs6/MIGS_eukaryote_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_samp_size + + + + +URI: [mixs.vocab:MIGS_eukaryote_samp_size](https://w3id.org/mixs/vocab/MIGS_eukaryote_samp_size) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sample_collect_device.md b/mixs6/MIGS_eukaryote_sample_collect_device.md new file mode 100644 index 00000000..1362ed1c --- /dev/null +++ b/mixs6/MIGS_eukaryote_sample_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_sample_collect_device + + + + +URI: [mixs.vocab:MIGS_eukaryote_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_eukaryote_sample_collect_device) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sample_collect_method.md b/mixs6/MIGS_eukaryote_sample_collect_method.md new file mode 100644 index 00000000..03b5f30e --- /dev/null +++ b/mixs6/MIGS_eukaryote_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_eukaryote_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_eukaryote_sample_collect_method) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sample_name.md b/mixs6/MIGS_eukaryote_sample_name.md new file mode 100644 index 00000000..7647d8a8 --- /dev/null +++ b/mixs6/MIGS_eukaryote_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_sample_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_sample_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_sample_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_seq_meth.md b/mixs6/MIGS_eukaryote_seq_meth.md new file mode 100644 index 00000000..d4b9d8e9 --- /dev/null +++ b/mixs6/MIGS_eukaryote_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_seq_meth + + + + +URI: [mixs.vocab:MIGS_eukaryote_seq_meth](https://w3id.org/mixs/vocab/MIGS_eukaryote_seq_meth) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sim_search_meth.md b/mixs6/MIGS_eukaryote_sim_search_meth.md new file mode 100644 index 00000000..c8c0d433 --- /dev/null +++ b/mixs6/MIGS_eukaryote_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_eukaryote_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_eukaryote_sim_search_meth) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sop.md b/mixs6/MIGS_eukaryote_sop.md new file mode 100644 index 00000000..fcd5ebf1 --- /dev/null +++ b/mixs6/MIGS_eukaryote_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_sop + + + + +URI: [mixs.vocab:MIGS_eukaryote_sop](https://w3id.org/mixs/vocab/MIGS_eukaryote_sop) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_source_mat_id.md b/mixs6/MIGS_eukaryote_source_mat_id.md new file mode 100644 index 00000000..89ed35a9 --- /dev/null +++ b/mixs6/MIGS_eukaryote_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_source_mat_id + + + + +URI: [mixs.vocab:MIGS_eukaryote_source_mat_id](https://w3id.org/mixs/vocab/MIGS_eukaryote_source_mat_id) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_specific_host.md b/mixs6/MIGS_eukaryote_specific_host.md new file mode 100644 index 00000000..dcde77ac --- /dev/null +++ b/mixs6/MIGS_eukaryote_specific_host.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_specific_host + + + + +URI: [mixs.vocab:MIGS_eukaryote_specific_host](https://w3id.org/mixs/vocab/MIGS_eukaryote_specific_host) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_submitted_to_insdc.md b/mixs6/MIGS_eukaryote_submitted_to_insdc.md new file mode 100644 index 00000000..c2c80a75 --- /dev/null +++ b/mixs6/MIGS_eukaryote_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_eukaryote_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_eukaryote_submitted_to_insdc) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_subspecf_gen_lin.md b/mixs6/MIGS_eukaryote_subspecf_gen_lin.md new file mode 100644 index 00000000..8877899c --- /dev/null +++ b/mixs6/MIGS_eukaryote_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_eukaryote_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_eukaryote_subspecf_gen_lin) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_tax_class.md b/mixs6/MIGS_eukaryote_tax_class.md new file mode 100644 index 00000000..b1655e70 --- /dev/null +++ b/mixs6/MIGS_eukaryote_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_tax_class + + + + +URI: [mixs.vocab:MIGS_eukaryote_tax_class](https://w3id.org/mixs/vocab/MIGS_eukaryote_tax_class) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_tax_ident.md b/mixs6/MIGS_eukaryote_tax_ident.md new file mode 100644 index 00000000..43f86760 --- /dev/null +++ b/mixs6/MIGS_eukaryote_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_tax_ident + + + + +URI: [mixs.vocab:MIGS_eukaryote_tax_ident](https://w3id.org/mixs/vocab/MIGS_eukaryote_tax_ident) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_trophic_level.md b/mixs6/MIGS_eukaryote_trophic_level.md new file mode 100644 index 00000000..a64dcb5a --- /dev/null +++ b/mixs6/MIGS_eukaryote_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_trophic_level + + + + +URI: [mixs.vocab:MIGS_eukaryote_trophic_level](https://w3id.org/mixs/vocab/MIGS_eukaryote_trophic_level) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_url.md b/mixs6/MIGS_eukaryote_url.md new file mode 100644 index 00000000..9af82372 --- /dev/null +++ b/mixs6/MIGS_eukaryote_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_url + + + + +URI: [mixs.vocab:MIGS_eukaryote_url](https://w3id.org/mixs/vocab/MIGS_eukaryote_url) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_org_sample_collect_device.md b/mixs6/MIGS_org_sample_collect_device.md new file mode 100644 index 00000000..fb357582 --- /dev/null +++ b/mixs6/MIGS_org_sample_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_sample_collect_device + + + + +URI: [mixs.vocab:MIGS_org_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_org_sample_collect_device) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/MIGS_org_sample_collect_method.md b/mixs6/MIGS_org_sample_collect_method.md new file mode 100644 index 00000000..00ddacfb --- /dev/null +++ b/mixs6/MIGS_org_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_org_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_org_sample_collect_method) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/MIGS_plant_adapters.md b/mixs6/MIGS_plant_adapters.md new file mode 100644 index 00000000..b9b79fc9 --- /dev/null +++ b/mixs6/MIGS_plant_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_adapters + + + + +URI: [mixs.vocab:MIGS_plant_adapters](https://w3id.org/mixs/vocab/MIGS_plant_adapters) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_annot.md b/mixs6/MIGS_plant_annot.md new file mode 100644 index 00000000..dd3c6fac --- /dev/null +++ b/mixs6/MIGS_plant_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_annot + + + + +URI: [mixs.vocab:MIGS_plant_annot](https://w3id.org/mixs/vocab/MIGS_plant_annot) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_assembly_name.md b/mixs6/MIGS_plant_assembly_name.md new file mode 100644 index 00000000..a14795dd --- /dev/null +++ b/mixs6/MIGS_plant_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_assembly_name + + + + +URI: [mixs.vocab:MIGS_plant_assembly_name](https://w3id.org/mixs/vocab/MIGS_plant_assembly_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_assembly_qual.md b/mixs6/MIGS_plant_assembly_qual.md new file mode 100644 index 00000000..7d5dda42 --- /dev/null +++ b/mixs6/MIGS_plant_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_assembly_qual + + + + +URI: [mixs.vocab:MIGS_plant_assembly_qual](https://w3id.org/mixs/vocab/MIGS_plant_assembly_qual) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_assembly_software.md b/mixs6/MIGS_plant_assembly_software.md new file mode 100644 index 00000000..89589ab7 --- /dev/null +++ b/mixs6/MIGS_plant_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_assembly_software + + + + +URI: [mixs.vocab:MIGS_plant_assembly_software](https://w3id.org/mixs/vocab/MIGS_plant_assembly_software) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_collection_date.md b/mixs6/MIGS_plant_collection_date.md new file mode 100644 index 00000000..6c3a079e --- /dev/null +++ b/mixs6/MIGS_plant_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_collection_date + + + + +URI: [mixs.vocab:MIGS_plant_collection_date](https://w3id.org/mixs/vocab/MIGS_plant_collection_date) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_compl_score.md b/mixs6/MIGS_plant_compl_score.md new file mode 100644 index 00000000..2f90e44d --- /dev/null +++ b/mixs6/MIGS_plant_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_compl_score + + + + +URI: [mixs.vocab:MIGS_plant_compl_score](https://w3id.org/mixs/vocab/MIGS_plant_compl_score) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_compl_software.md b/mixs6/MIGS_plant_compl_software.md new file mode 100644 index 00000000..b369a96d --- /dev/null +++ b/mixs6/MIGS_plant_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_compl_software + + + + +URI: [mixs.vocab:MIGS_plant_compl_software](https://w3id.org/mixs/vocab/MIGS_plant_compl_software) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_encoded_traits.md b/mixs6/MIGS_plant_encoded_traits.md new file mode 100644 index 00000000..953db827 --- /dev/null +++ b/mixs6/MIGS_plant_encoded_traits.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_encoded_traits + + + + +URI: [mixs.vocab:MIGS_plant_encoded_traits](https://w3id.org/mixs/vocab/MIGS_plant_encoded_traits) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_env_broad_scale.md b/mixs6/MIGS_plant_env_broad_scale.md new file mode 100644 index 00000000..f3f6b225 --- /dev/null +++ b/mixs6/MIGS_plant_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_plant_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_plant_env_broad_scale) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_env_local_scale.md b/mixs6/MIGS_plant_env_local_scale.md new file mode 100644 index 00000000..f97a444b --- /dev/null +++ b/mixs6/MIGS_plant_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_env_local_scale + + + + +URI: [mixs.vocab:MIGS_plant_env_local_scale](https://w3id.org/mixs/vocab/MIGS_plant_env_local_scale) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_env_medium.md b/mixs6/MIGS_plant_env_medium.md new file mode 100644 index 00000000..c1e6c02f --- /dev/null +++ b/mixs6/MIGS_plant_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_env_medium + + + + +URI: [mixs.vocab:MIGS_plant_env_medium](https://w3id.org/mixs/vocab/MIGS_plant_env_medium) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_env_package.md b/mixs6/MIGS_plant_env_package.md new file mode 100644 index 00000000..1c332eb2 --- /dev/null +++ b/mixs6/MIGS_plant_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_env_package + + + + +URI: [mixs.vocab:MIGS_plant_env_package](https://w3id.org/mixs/vocab/MIGS_plant_env_package) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_estimated_size.md b/mixs6/MIGS_plant_estimated_size.md new file mode 100644 index 00000000..3e506e0d --- /dev/null +++ b/mixs6/MIGS_plant_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_estimated_size + + + + +URI: [mixs.vocab:MIGS_plant_estimated_size](https://w3id.org/mixs/vocab/MIGS_plant_estimated_size) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_experimental_factor.md b/mixs6/MIGS_plant_experimental_factor.md new file mode 100644 index 00000000..2045f70b --- /dev/null +++ b/mixs6/MIGS_plant_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_experimental_factor + + + + +URI: [mixs.vocab:MIGS_plant_experimental_factor](https://w3id.org/mixs/vocab/MIGS_plant_experimental_factor) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_feat_pred.md b/mixs6/MIGS_plant_feat_pred.md new file mode 100644 index 00000000..b4146b1a --- /dev/null +++ b/mixs6/MIGS_plant_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_feat_pred + + + + +URI: [mixs.vocab:MIGS_plant_feat_pred](https://w3id.org/mixs/vocab/MIGS_plant_feat_pred) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_geo_loc_name.md b/mixs6/MIGS_plant_geo_loc_name.md new file mode 100644 index 00000000..6122fb42 --- /dev/null +++ b/mixs6/MIGS_plant_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_plant_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_plant_geo_loc_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_host_spec_range.md b/mixs6/MIGS_plant_host_spec_range.md new file mode 100644 index 00000000..986f5845 --- /dev/null +++ b/mixs6/MIGS_plant_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_host_spec_range + + + + +URI: [mixs.vocab:MIGS_plant_host_spec_range](https://w3id.org/mixs/vocab/MIGS_plant_host_spec_range) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_investigation_type.md b/mixs6/MIGS_plant_investigation_type.md new file mode 100644 index 00000000..05ca7ce2 --- /dev/null +++ b/mixs6/MIGS_plant_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_investigation_type + + + + +URI: [mixs.vocab:MIGS_plant_investigation_type](https://w3id.org/mixs/vocab/MIGS_plant_investigation_type) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_isol_growth_condt.md b/mixs6/MIGS_plant_isol_growth_condt.md new file mode 100644 index 00000000..a1ad3590 --- /dev/null +++ b/mixs6/MIGS_plant_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_plant_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_plant_isol_growth_condt) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lat_lon.md b/mixs6/MIGS_plant_lat_lon.md new file mode 100644 index 00000000..93a3b91b --- /dev/null +++ b/mixs6/MIGS_plant_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_lat_lon + + + + +URI: [mixs.vocab:MIGS_plant_lat_lon](https://w3id.org/mixs/vocab/MIGS_plant_lat_lon) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_layout.md b/mixs6/MIGS_plant_lib_layout.md new file mode 100644 index 00000000..dc22b890 --- /dev/null +++ b/mixs6/MIGS_plant_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_layout + + + + +URI: [mixs.vocab:MIGS_plant_lib_layout](https://w3id.org/mixs/vocab/MIGS_plant_lib_layout) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_reads_seqd.md b/mixs6/MIGS_plant_lib_reads_seqd.md new file mode 100644 index 00000000..71af3d1b --- /dev/null +++ b/mixs6/MIGS_plant_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_plant_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_plant_lib_reads_seqd) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_screen.md b/mixs6/MIGS_plant_lib_screen.md new file mode 100644 index 00000000..83a688b9 --- /dev/null +++ b/mixs6/MIGS_plant_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_screen + + + + +URI: [mixs.vocab:MIGS_plant_lib_screen](https://w3id.org/mixs/vocab/MIGS_plant_lib_screen) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_size.md b/mixs6/MIGS_plant_lib_size.md new file mode 100644 index 00000000..8a271c88 --- /dev/null +++ b/mixs6/MIGS_plant_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_size + + + + +URI: [mixs.vocab:MIGS_plant_lib_size](https://w3id.org/mixs/vocab/MIGS_plant_lib_size) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_vector.md b/mixs6/MIGS_plant_lib_vector.md new file mode 100644 index 00000000..51ee6bf3 --- /dev/null +++ b/mixs6/MIGS_plant_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_vector + + + + +URI: [mixs.vocab:MIGS_plant_lib_vector](https://w3id.org/mixs/vocab/MIGS_plant_lib_vector) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_nucl_acid_amp.md b/mixs6/MIGS_plant_nucl_acid_amp.md new file mode 100644 index 00000000..ceb8ceb1 --- /dev/null +++ b/mixs6/MIGS_plant_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_plant_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_plant_nucl_acid_amp) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_nucl_acid_ext.md b/mixs6/MIGS_plant_nucl_acid_ext.md new file mode 100644 index 00000000..0a15a1ff --- /dev/null +++ b/mixs6/MIGS_plant_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_plant_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_plant_nucl_acid_ext) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_number_contig.md b/mixs6/MIGS_plant_number_contig.md new file mode 100644 index 00000000..e6d8bceb --- /dev/null +++ b/mixs6/MIGS_plant_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_number_contig + + + + +URI: [mixs.vocab:MIGS_plant_number_contig](https://w3id.org/mixs/vocab/MIGS_plant_number_contig) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_project_name.md b/mixs6/MIGS_plant_project_name.md new file mode 100644 index 00000000..66133a7c --- /dev/null +++ b/mixs6/MIGS_plant_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_project_name + + + + +URI: [mixs.vocab:MIGS_plant_project_name](https://w3id.org/mixs/vocab/MIGS_plant_project_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_propagation.md b/mixs6/MIGS_plant_propagation.md new file mode 100644 index 00000000..e7014b7a --- /dev/null +++ b/mixs6/MIGS_plant_propagation.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_propagation + + + + +URI: [mixs.vocab:MIGS_plant_propagation](https://w3id.org/mixs/vocab/MIGS_plant_propagation) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_ref_biomaterial.md b/mixs6/MIGS_plant_ref_biomaterial.md new file mode 100644 index 00000000..762537d4 --- /dev/null +++ b/mixs6/MIGS_plant_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_plant_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_plant_ref_biomaterial) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_ref_db.md b/mixs6/MIGS_plant_ref_db.md new file mode 100644 index 00000000..817da0d8 --- /dev/null +++ b/mixs6/MIGS_plant_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_ref_db + + + + +URI: [mixs.vocab:MIGS_plant_ref_db](https://w3id.org/mixs/vocab/MIGS_plant_ref_db) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_samp_mat_process.md b/mixs6/MIGS_plant_samp_mat_process.md new file mode 100644 index 00000000..d7f7bb5f --- /dev/null +++ b/mixs6/MIGS_plant_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_plant_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_plant_samp_mat_process) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_samp_size.md b/mixs6/MIGS_plant_samp_size.md new file mode 100644 index 00000000..6a08be13 --- /dev/null +++ b/mixs6/MIGS_plant_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_samp_size + + + + +URI: [mixs.vocab:MIGS_plant_samp_size](https://w3id.org/mixs/vocab/MIGS_plant_samp_size) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sample_collect_device.md b/mixs6/MIGS_plant_sample_collect_device.md new file mode 100644 index 00000000..053e90b0 --- /dev/null +++ b/mixs6/MIGS_plant_sample_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_sample_collect_device + + + + +URI: [mixs.vocab:MIGS_plant_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_plant_sample_collect_device) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sample_collect_method.md b/mixs6/MIGS_plant_sample_collect_method.md new file mode 100644 index 00000000..aad27a5d --- /dev/null +++ b/mixs6/MIGS_plant_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_plant_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_plant_sample_collect_method) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sample_name.md b/mixs6/MIGS_plant_sample_name.md new file mode 100644 index 00000000..dbf67ad6 --- /dev/null +++ b/mixs6/MIGS_plant_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_sample_name + + + + +URI: [mixs.vocab:MIGS_plant_sample_name](https://w3id.org/mixs/vocab/MIGS_plant_sample_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_seq_meth.md b/mixs6/MIGS_plant_seq_meth.md new file mode 100644 index 00000000..8588e681 --- /dev/null +++ b/mixs6/MIGS_plant_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_seq_meth + + + + +URI: [mixs.vocab:MIGS_plant_seq_meth](https://w3id.org/mixs/vocab/MIGS_plant_seq_meth) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sim_search_meth.md b/mixs6/MIGS_plant_sim_search_meth.md new file mode 100644 index 00000000..de0f4f75 --- /dev/null +++ b/mixs6/MIGS_plant_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_plant_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_plant_sim_search_meth) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sop.md b/mixs6/MIGS_plant_sop.md new file mode 100644 index 00000000..b64e28c5 --- /dev/null +++ b/mixs6/MIGS_plant_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_sop + + + + +URI: [mixs.vocab:MIGS_plant_sop](https://w3id.org/mixs/vocab/MIGS_plant_sop) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_source_mat_id.md b/mixs6/MIGS_plant_source_mat_id.md new file mode 100644 index 00000000..be275e0a --- /dev/null +++ b/mixs6/MIGS_plant_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_source_mat_id + + + + +URI: [mixs.vocab:MIGS_plant_source_mat_id](https://w3id.org/mixs/vocab/MIGS_plant_source_mat_id) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_specific_host.md b/mixs6/MIGS_plant_specific_host.md new file mode 100644 index 00000000..2668f9b3 --- /dev/null +++ b/mixs6/MIGS_plant_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_specific_host + + + + +URI: [mixs.vocab:MIGS_plant_specific_host](https://w3id.org/mixs/vocab/MIGS_plant_specific_host) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_submitted_to_insdc.md b/mixs6/MIGS_plant_submitted_to_insdc.md new file mode 100644 index 00000000..80dc3910 --- /dev/null +++ b/mixs6/MIGS_plant_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_plant_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_plant_submitted_to_insdc) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_subspecf_gen_lin.md b/mixs6/MIGS_plant_subspecf_gen_lin.md new file mode 100644 index 00000000..917376da --- /dev/null +++ b/mixs6/MIGS_plant_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_plant_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_plant_subspecf_gen_lin) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_tax_class.md b/mixs6/MIGS_plant_tax_class.md new file mode 100644 index 00000000..fdd028f7 --- /dev/null +++ b/mixs6/MIGS_plant_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_tax_class + + + + +URI: [mixs.vocab:MIGS_plant_tax_class](https://w3id.org/mixs/vocab/MIGS_plant_tax_class) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_tax_ident.md b/mixs6/MIGS_plant_tax_ident.md new file mode 100644 index 00000000..b248a803 --- /dev/null +++ b/mixs6/MIGS_plant_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_tax_ident + + + + +URI: [mixs.vocab:MIGS_plant_tax_ident](https://w3id.org/mixs/vocab/MIGS_plant_tax_ident) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_url.md b/mixs6/MIGS_plant_url.md new file mode 100644 index 00000000..3319deb6 --- /dev/null +++ b/mixs6/MIGS_plant_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_url + + + + +URI: [mixs.vocab:MIGS_plant_url](https://w3id.org/mixs/vocab/MIGS_plant_url) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_adapters.md b/mixs6/MIGS_virus_adapters.md new file mode 100644 index 00000000..3af4bb77 --- /dev/null +++ b/mixs6/MIGS_virus_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_adapters + + + + +URI: [mixs.vocab:MIGS_virus_adapters](https://w3id.org/mixs/vocab/MIGS_virus_adapters) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_annot.md b/mixs6/MIGS_virus_annot.md new file mode 100644 index 00000000..83ddd3ec --- /dev/null +++ b/mixs6/MIGS_virus_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_annot + + + + +URI: [mixs.vocab:MIGS_virus_annot](https://w3id.org/mixs/vocab/MIGS_virus_annot) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_assembly_name.md b/mixs6/MIGS_virus_assembly_name.md new file mode 100644 index 00000000..a1fbc0f7 --- /dev/null +++ b/mixs6/MIGS_virus_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_assembly_name + + + + +URI: [mixs.vocab:MIGS_virus_assembly_name](https://w3id.org/mixs/vocab/MIGS_virus_assembly_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_assembly_qual.md b/mixs6/MIGS_virus_assembly_qual.md new file mode 100644 index 00000000..076e135b --- /dev/null +++ b/mixs6/MIGS_virus_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_assembly_qual + + + + +URI: [mixs.vocab:MIGS_virus_assembly_qual](https://w3id.org/mixs/vocab/MIGS_virus_assembly_qual) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_assembly_software.md b/mixs6/MIGS_virus_assembly_software.md new file mode 100644 index 00000000..d3cb98a2 --- /dev/null +++ b/mixs6/MIGS_virus_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_assembly_software + + + + +URI: [mixs.vocab:MIGS_virus_assembly_software](https://w3id.org/mixs/vocab/MIGS_virus_assembly_software) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_biotic_relationship.md b/mixs6/MIGS_virus_biotic_relationship.md new file mode 100644 index 00000000..b0ab80c6 --- /dev/null +++ b/mixs6/MIGS_virus_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_biotic_relationship + + + + +URI: [mixs.vocab:MIGS_virus_biotic_relationship](https://w3id.org/mixs/vocab/MIGS_virus_biotic_relationship) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_collection_date.md b/mixs6/MIGS_virus_collection_date.md new file mode 100644 index 00000000..a81cfb4d --- /dev/null +++ b/mixs6/MIGS_virus_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_collection_date + + + + +URI: [mixs.vocab:MIGS_virus_collection_date](https://w3id.org/mixs/vocab/MIGS_virus_collection_date) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_compl_score.md b/mixs6/MIGS_virus_compl_score.md new file mode 100644 index 00000000..8c26a4a7 --- /dev/null +++ b/mixs6/MIGS_virus_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_compl_score + + + + +URI: [mixs.vocab:MIGS_virus_compl_score](https://w3id.org/mixs/vocab/MIGS_virus_compl_score) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_compl_software.md b/mixs6/MIGS_virus_compl_software.md new file mode 100644 index 00000000..a25b73e0 --- /dev/null +++ b/mixs6/MIGS_virus_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_compl_software + + + + +URI: [mixs.vocab:MIGS_virus_compl_software](https://w3id.org/mixs/vocab/MIGS_virus_compl_software) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_encoded_traits.md b/mixs6/MIGS_virus_encoded_traits.md new file mode 100644 index 00000000..abea9dd2 --- /dev/null +++ b/mixs6/MIGS_virus_encoded_traits.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_encoded_traits + + + + +URI: [mixs.vocab:MIGS_virus_encoded_traits](https://w3id.org/mixs/vocab/MIGS_virus_encoded_traits) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_env_broad_scale.md b/mixs6/MIGS_virus_env_broad_scale.md new file mode 100644 index 00000000..2f82307a --- /dev/null +++ b/mixs6/MIGS_virus_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_virus_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_virus_env_broad_scale) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_env_local_scale.md b/mixs6/MIGS_virus_env_local_scale.md new file mode 100644 index 00000000..6161f73f --- /dev/null +++ b/mixs6/MIGS_virus_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_env_local_scale + + + + +URI: [mixs.vocab:MIGS_virus_env_local_scale](https://w3id.org/mixs/vocab/MIGS_virus_env_local_scale) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_env_medium.md b/mixs6/MIGS_virus_env_medium.md new file mode 100644 index 00000000..04d6c460 --- /dev/null +++ b/mixs6/MIGS_virus_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_env_medium + + + + +URI: [mixs.vocab:MIGS_virus_env_medium](https://w3id.org/mixs/vocab/MIGS_virus_env_medium) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_env_package.md b/mixs6/MIGS_virus_env_package.md new file mode 100644 index 00000000..821760f5 --- /dev/null +++ b/mixs6/MIGS_virus_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_env_package + + + + +URI: [mixs.vocab:MIGS_virus_env_package](https://w3id.org/mixs/vocab/MIGS_virus_env_package) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_estimated_size.md b/mixs6/MIGS_virus_estimated_size.md new file mode 100644 index 00000000..a1dbdbe5 --- /dev/null +++ b/mixs6/MIGS_virus_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_estimated_size + + + + +URI: [mixs.vocab:MIGS_virus_estimated_size](https://w3id.org/mixs/vocab/MIGS_virus_estimated_size) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_experimental_factor.md b/mixs6/MIGS_virus_experimental_factor.md new file mode 100644 index 00000000..e4fe55c9 --- /dev/null +++ b/mixs6/MIGS_virus_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_experimental_factor + + + + +URI: [mixs.vocab:MIGS_virus_experimental_factor](https://w3id.org/mixs/vocab/MIGS_virus_experimental_factor) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_feat_pred.md b/mixs6/MIGS_virus_feat_pred.md new file mode 100644 index 00000000..efe080e6 --- /dev/null +++ b/mixs6/MIGS_virus_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_feat_pred + + + + +URI: [mixs.vocab:MIGS_virus_feat_pred](https://w3id.org/mixs/vocab/MIGS_virus_feat_pred) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_geo_loc_name.md b/mixs6/MIGS_virus_geo_loc_name.md new file mode 100644 index 00000000..1a2b6e8e --- /dev/null +++ b/mixs6/MIGS_virus_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_virus_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_virus_geo_loc_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_health_disease_stat.md b/mixs6/MIGS_virus_health_disease_stat.md new file mode 100644 index 00000000..bb108f40 --- /dev/null +++ b/mixs6/MIGS_virus_health_disease_stat.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_health_disease_stat + + + + +URI: [mixs.vocab:MIGS_virus_health_disease_stat](https://w3id.org/mixs/vocab/MIGS_virus_health_disease_stat) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_host_spec_range.md b/mixs6/MIGS_virus_host_spec_range.md new file mode 100644 index 00000000..937559d3 --- /dev/null +++ b/mixs6/MIGS_virus_host_spec_range.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_host_spec_range + + + + +URI: [mixs.vocab:MIGS_virus_host_spec_range](https://w3id.org/mixs/vocab/MIGS_virus_host_spec_range) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_investigation_type.md b/mixs6/MIGS_virus_investigation_type.md new file mode 100644 index 00000000..d3b016f3 --- /dev/null +++ b/mixs6/MIGS_virus_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_investigation_type + + + + +URI: [mixs.vocab:MIGS_virus_investigation_type](https://w3id.org/mixs/vocab/MIGS_virus_investigation_type) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_isol_growth_condt.md b/mixs6/MIGS_virus_isol_growth_condt.md new file mode 100644 index 00000000..03339b2a --- /dev/null +++ b/mixs6/MIGS_virus_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_virus_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_virus_isol_growth_condt) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lat_lon.md b/mixs6/MIGS_virus_lat_lon.md new file mode 100644 index 00000000..b365a499 --- /dev/null +++ b/mixs6/MIGS_virus_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_lat_lon + + + + +URI: [mixs.vocab:MIGS_virus_lat_lon](https://w3id.org/mixs/vocab/MIGS_virus_lat_lon) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_layout.md b/mixs6/MIGS_virus_lib_layout.md new file mode 100644 index 00000000..1a5dacdd --- /dev/null +++ b/mixs6/MIGS_virus_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_layout + + + + +URI: [mixs.vocab:MIGS_virus_lib_layout](https://w3id.org/mixs/vocab/MIGS_virus_lib_layout) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_reads_seqd.md b/mixs6/MIGS_virus_lib_reads_seqd.md new file mode 100644 index 00000000..c8d802d5 --- /dev/null +++ b/mixs6/MIGS_virus_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_virus_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_virus_lib_reads_seqd) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_screen.md b/mixs6/MIGS_virus_lib_screen.md new file mode 100644 index 00000000..124909fa --- /dev/null +++ b/mixs6/MIGS_virus_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_screen + + + + +URI: [mixs.vocab:MIGS_virus_lib_screen](https://w3id.org/mixs/vocab/MIGS_virus_lib_screen) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_size.md b/mixs6/MIGS_virus_lib_size.md new file mode 100644 index 00000000..bf19fdce --- /dev/null +++ b/mixs6/MIGS_virus_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_size + + + + +URI: [mixs.vocab:MIGS_virus_lib_size](https://w3id.org/mixs/vocab/MIGS_virus_lib_size) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_vector.md b/mixs6/MIGS_virus_lib_vector.md new file mode 100644 index 00000000..3b23e00e --- /dev/null +++ b/mixs6/MIGS_virus_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_vector + + + + +URI: [mixs.vocab:MIGS_virus_lib_vector](https://w3id.org/mixs/vocab/MIGS_virus_lib_vector) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_nucl_acid_amp.md b/mixs6/MIGS_virus_nucl_acid_amp.md new file mode 100644 index 00000000..efee8686 --- /dev/null +++ b/mixs6/MIGS_virus_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_virus_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_virus_nucl_acid_amp) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_nucl_acid_ext.md b/mixs6/MIGS_virus_nucl_acid_ext.md new file mode 100644 index 00000000..e47ef973 --- /dev/null +++ b/mixs6/MIGS_virus_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_virus_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_virus_nucl_acid_ext) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_num_replicons.md b/mixs6/MIGS_virus_num_replicons.md new file mode 100644 index 00000000..36003fc3 --- /dev/null +++ b/mixs6/MIGS_virus_num_replicons.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_num_replicons + + + + +URI: [mixs.vocab:MIGS_virus_num_replicons](https://w3id.org/mixs/vocab/MIGS_virus_num_replicons) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_number_contig.md b/mixs6/MIGS_virus_number_contig.md new file mode 100644 index 00000000..5b343998 --- /dev/null +++ b/mixs6/MIGS_virus_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_number_contig + + + + +URI: [mixs.vocab:MIGS_virus_number_contig](https://w3id.org/mixs/vocab/MIGS_virus_number_contig) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_pathogenicity.md b/mixs6/MIGS_virus_pathogenicity.md new file mode 100644 index 00000000..c030db33 --- /dev/null +++ b/mixs6/MIGS_virus_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_pathogenicity + + + + +URI: [mixs.vocab:MIGS_virus_pathogenicity](https://w3id.org/mixs/vocab/MIGS_virus_pathogenicity) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_project_name.md b/mixs6/MIGS_virus_project_name.md new file mode 100644 index 00000000..b09e6204 --- /dev/null +++ b/mixs6/MIGS_virus_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_project_name + + + + +URI: [mixs.vocab:MIGS_virus_project_name](https://w3id.org/mixs/vocab/MIGS_virus_project_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_propagation.md b/mixs6/MIGS_virus_propagation.md new file mode 100644 index 00000000..feb5d620 --- /dev/null +++ b/mixs6/MIGS_virus_propagation.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_propagation + + + + +URI: [mixs.vocab:MIGS_virus_propagation](https://w3id.org/mixs/vocab/MIGS_virus_propagation) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_ref_biomaterial.md b/mixs6/MIGS_virus_ref_biomaterial.md new file mode 100644 index 00000000..e9923aa7 --- /dev/null +++ b/mixs6/MIGS_virus_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_virus_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_virus_ref_biomaterial) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_ref_db.md b/mixs6/MIGS_virus_ref_db.md new file mode 100644 index 00000000..294be230 --- /dev/null +++ b/mixs6/MIGS_virus_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_ref_db + + + + +URI: [mixs.vocab:MIGS_virus_ref_db](https://w3id.org/mixs/vocab/MIGS_virus_ref_db) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_samp_mat_process.md b/mixs6/MIGS_virus_samp_mat_process.md new file mode 100644 index 00000000..824b26cd --- /dev/null +++ b/mixs6/MIGS_virus_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_virus_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_virus_samp_mat_process) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_samp_size.md b/mixs6/MIGS_virus_samp_size.md new file mode 100644 index 00000000..063c0a84 --- /dev/null +++ b/mixs6/MIGS_virus_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_samp_size + + + + +URI: [mixs.vocab:MIGS_virus_samp_size](https://w3id.org/mixs/vocab/MIGS_virus_samp_size) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sample_collect_device.md b/mixs6/MIGS_virus_sample_collect_device.md new file mode 100644 index 00000000..7fc3bbfa --- /dev/null +++ b/mixs6/MIGS_virus_sample_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_sample_collect_device + + + + +URI: [mixs.vocab:MIGS_virus_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_virus_sample_collect_device) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sample_collect_method.md b/mixs6/MIGS_virus_sample_collect_method.md new file mode 100644 index 00000000..8c362c89 --- /dev/null +++ b/mixs6/MIGS_virus_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_virus_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_virus_sample_collect_method) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sample_name.md b/mixs6/MIGS_virus_sample_name.md new file mode 100644 index 00000000..278617b5 --- /dev/null +++ b/mixs6/MIGS_virus_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_sample_name + + + + +URI: [mixs.vocab:MIGS_virus_sample_name](https://w3id.org/mixs/vocab/MIGS_virus_sample_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_seq_meth.md b/mixs6/MIGS_virus_seq_meth.md new file mode 100644 index 00000000..12a54f20 --- /dev/null +++ b/mixs6/MIGS_virus_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_seq_meth + + + + +URI: [mixs.vocab:MIGS_virus_seq_meth](https://w3id.org/mixs/vocab/MIGS_virus_seq_meth) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sim_search_meth.md b/mixs6/MIGS_virus_sim_search_meth.md new file mode 100644 index 00000000..7cedab79 --- /dev/null +++ b/mixs6/MIGS_virus_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_virus_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_virus_sim_search_meth) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sop.md b/mixs6/MIGS_virus_sop.md new file mode 100644 index 00000000..b2833d26 --- /dev/null +++ b/mixs6/MIGS_virus_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_sop + + + + +URI: [mixs.vocab:MIGS_virus_sop](https://w3id.org/mixs/vocab/MIGS_virus_sop) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_source_mat_id.md b/mixs6/MIGS_virus_source_mat_id.md new file mode 100644 index 00000000..1c6ae3e1 --- /dev/null +++ b/mixs6/MIGS_virus_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_source_mat_id + + + + +URI: [mixs.vocab:MIGS_virus_source_mat_id](https://w3id.org/mixs/vocab/MIGS_virus_source_mat_id) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_specific_host.md b/mixs6/MIGS_virus_specific_host.md new file mode 100644 index 00000000..a6f23215 --- /dev/null +++ b/mixs6/MIGS_virus_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_specific_host + + + + +URI: [mixs.vocab:MIGS_virus_specific_host](https://w3id.org/mixs/vocab/MIGS_virus_specific_host) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_submitted_to_insdc.md b/mixs6/MIGS_virus_submitted_to_insdc.md new file mode 100644 index 00000000..a7018b35 --- /dev/null +++ b/mixs6/MIGS_virus_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_virus_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_virus_submitted_to_insdc) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_subspecf_gen_lin.md b/mixs6/MIGS_virus_subspecf_gen_lin.md new file mode 100644 index 00000000..c31ace14 --- /dev/null +++ b/mixs6/MIGS_virus_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_virus_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_virus_subspecf_gen_lin) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_tax_class.md b/mixs6/MIGS_virus_tax_class.md new file mode 100644 index 00000000..acbdd246 --- /dev/null +++ b/mixs6/MIGS_virus_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_tax_class + + + + +URI: [mixs.vocab:MIGS_virus_tax_class](https://w3id.org/mixs/vocab/MIGS_virus_tax_class) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_tax_ident.md b/mixs6/MIGS_virus_tax_ident.md new file mode 100644 index 00000000..b7e9d7cb --- /dev/null +++ b/mixs6/MIGS_virus_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_tax_ident + + + + +URI: [mixs.vocab:MIGS_virus_tax_ident](https://w3id.org/mixs/vocab/MIGS_virus_tax_ident) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_url.md b/mixs6/MIGS_virus_url.md new file mode 100644 index 00000000..8eacf6b3 --- /dev/null +++ b/mixs6/MIGS_virus_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_url + + + + +URI: [mixs.vocab:MIGS_virus_url](https://w3id.org/mixs/vocab/MIGS_virus_url) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_virus_enrich_appr.md b/mixs6/MIGS_virus_virus_enrich_appr.md new file mode 100644 index 00000000..2452475a --- /dev/null +++ b/mixs6/MIGS_virus_virus_enrich_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_virus_enrich_appr + + + + +URI: [mixs.vocab:MIGS_virus_virus_enrich_appr](https://w3id.org/mixs/vocab/MIGS_virus_virus_enrich_appr) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [virus_enrich_appr](virus_enrich_appr.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMAG_sample_collect_device.md b/mixs6/MIMAG_sample_collect_device.md new file mode 100644 index 00000000..3b9f9ea8 --- /dev/null +++ b/mixs6/MIMAG_sample_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_sample_collect_device + + + + +URI: [mixs.vocab:MIMAG_sample_collect_device](https://w3id.org/mixs/vocab/MIMAG_sample_collect_device) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMAG_sample_collect_method.md b/mixs6/MIMAG_sample_collect_method.md new file mode 100644 index 00000000..742757c4 --- /dev/null +++ b/mixs6/MIMAG_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_sample_collect_method + + + + +URI: [mixs.vocab:MIMAG_sample_collect_method](https://w3id.org/mixs/vocab/MIMAG_sample_collect_method) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKSSpecimen.md b/mixs6/MIMARKSSpecimen.md new file mode 100644 index 00000000..8f61465c --- /dev/null +++ b/mixs6/MIMARKSSpecimen.md @@ -0,0 +1,122 @@ + +# Class: MIMARKSSpecimen + + +Minimal Information about a Marker Specimen: specimen + +URI: [mixs.vocab:MIMARKSSpecimen](https://w3id.org/mixs/vocab/MIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SoilMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SedimentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-skinMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-oralMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-gutMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Host-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[AirMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[WaterMIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen],[SoilMIMARKSSpecimen],[SedimentMIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen],[Human-skinMIMARKSSpecimen],[Human-oralMIMARKSSpecimen],[Human-gutMIMARKSSpecimen],[Human-associatedMIMARKSSpecimen],[Host-associatedMIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen],[AirMIMARKSSpecimen]) + +## Mixin for + + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package air + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package built environment + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package host-associated + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-associated + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-gut + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-oral + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-skin + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-vaginal + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package plant-associated + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package soil + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package wastewater_sludge + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞collection_date](MIMARKS_specimen_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIMARKS specimen➞env_broad_scale](MIMARKS_specimen_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞env_local_scale](MIMARKS_specimen_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞env_medium](MIMARKS_specimen_env_medium.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞geo_loc_name](MIMARKS_specimen_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + * [MIMARKS specimen➞lat_lon](MIMARKS_specimen_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIMARKS.specimen | + diff --git a/mixs6/MIMARKSSurvey.md b/mixs6/MIMARKSSurvey.md new file mode 100644 index 00000000..b57a5821 --- /dev/null +++ b/mixs6/MIMARKSSurvey.md @@ -0,0 +1,114 @@ + +# Class: MIMARKSSurvey + + +Minimal Information about a Marker Specimen: survey + +URI: [mixs.vocab:MIMARKSSurvey](https://w3id.org/mixs/vocab/MIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SoilMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SedimentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Plant-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-vaginalMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-skinMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-oralMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-gutMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Host-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[AirMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[WaterMIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey],[SoilMIMARKSSurvey],[SedimentMIMARKSSurvey],[Plant-associatedMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey],[Human-vaginalMIMARKSSurvey],[Human-skinMIMARKSSurvey],[Human-oralMIMARKSSurvey],[Human-gutMIMARKSSurvey],[Human-associatedMIMARKSSurvey],[Host-associatedMIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey],[AirMIMARKSSurvey]) + +## Mixin for + + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package air + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package built environment + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package host-associated + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-associated + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-gut + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-oral + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-skin + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-vaginal + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package plant-associated + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package sediment + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package wastewater_sludge + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞collection_date](MIMARKS_survey_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIMARKS survey➞env_broad_scale](MIMARKS_survey_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞env_local_scale](MIMARKS_survey_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞env_medium](MIMARKS_survey_env_medium.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞geo_loc_name](MIMARKS_survey_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞lat_lon](MIMARKS_survey_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIMARKS.survey | + diff --git a/mixs6/MIMARKS_specimen_adapters.md b/mixs6/MIMARKS_specimen_adapters.md new file mode 100644 index 00000000..a713e106 --- /dev/null +++ b/mixs6/MIMARKS_specimen_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_adapters + + + + +URI: [mixs.vocab:MIMARKS_specimen_adapters](https://w3id.org/mixs/vocab/MIMARKS_specimen_adapters) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_assembly_software.md b/mixs6/MIMARKS_specimen_assembly_software.md new file mode 100644 index 00000000..88896b68 --- /dev/null +++ b/mixs6/MIMARKS_specimen_assembly_software.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_assembly_software + + + + +URI: [mixs.vocab:MIMARKS_specimen_assembly_software](https://w3id.org/mixs/vocab/MIMARKS_specimen_assembly_software) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_chimera_check.md b/mixs6/MIMARKS_specimen_chimera_check.md new file mode 100644 index 00000000..26915f53 --- /dev/null +++ b/mixs6/MIMARKS_specimen_chimera_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_chimera_check + + + + +URI: [mixs.vocab:MIMARKS_specimen_chimera_check](https://w3id.org/mixs/vocab/MIMARKS_specimen_chimera_check) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [chimera_check](chimera_check.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_collection_date.md b/mixs6/MIMARKS_specimen_collection_date.md new file mode 100644 index 00000000..2a056cd5 --- /dev/null +++ b/mixs6/MIMARKS_specimen_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_collection_date + + + + +URI: [mixs.vocab:MIMARKS_specimen_collection_date](https://w3id.org/mixs/vocab/MIMARKS_specimen_collection_date) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_broad_scale.md b/mixs6/MIMARKS_specimen_env_broad_scale.md new file mode 100644 index 00000000..b7c81d27 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_env_broad_scale + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_broad_scale](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_broad_scale) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_local_scale.md b/mixs6/MIMARKS_specimen_env_local_scale.md new file mode 100644 index 00000000..523f9db4 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_env_local_scale + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_local_scale](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_local_scale) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_medium.md b/mixs6/MIMARKS_specimen_env_medium.md new file mode 100644 index 00000000..c54c5057 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_env_medium + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_medium](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_medium) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_package.md b/mixs6/MIMARKS_specimen_env_package.md new file mode 100644 index 00000000..c101ddb9 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_env_package + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_package](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_package) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_experimental_factor.md b/mixs6/MIMARKS_specimen_experimental_factor.md new file mode 100644 index 00000000..300e708e --- /dev/null +++ b/mixs6/MIMARKS_specimen_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_experimental_factor + + + + +URI: [mixs.vocab:MIMARKS_specimen_experimental_factor](https://w3id.org/mixs/vocab/MIMARKS_specimen_experimental_factor) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_geo_loc_name.md b/mixs6/MIMARKS_specimen_geo_loc_name.md new file mode 100644 index 00000000..950adeef --- /dev/null +++ b/mixs6/MIMARKS_specimen_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_geo_loc_name + + + + +URI: [mixs.vocab:MIMARKS_specimen_geo_loc_name](https://w3id.org/mixs/vocab/MIMARKS_specimen_geo_loc_name) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_investigation_type.md b/mixs6/MIMARKS_specimen_investigation_type.md new file mode 100644 index 00000000..5a407c8c --- /dev/null +++ b/mixs6/MIMARKS_specimen_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_investigation_type + + + + +URI: [mixs.vocab:MIMARKS_specimen_investigation_type](https://w3id.org/mixs/vocab/MIMARKS_specimen_investigation_type) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_lat_lon.md b/mixs6/MIMARKS_specimen_lat_lon.md new file mode 100644 index 00000000..f764eb41 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_lat_lon + + + + +URI: [mixs.vocab:MIMARKS_specimen_lat_lon](https://w3id.org/mixs/vocab/MIMARKS_specimen_lat_lon) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_lib_layout.md b/mixs6/MIMARKS_specimen_lib_layout.md new file mode 100644 index 00000000..060caaf4 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_layout + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_layout](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_layout) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_reads_seqd.md b/mixs6/MIMARKS_specimen_lib_reads_seqd.md new file mode 100644 index 00000000..2ddfc09e --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_reads_seqd + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_reads_seqd](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_reads_seqd) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_screen.md b/mixs6/MIMARKS_specimen_lib_screen.md new file mode 100644 index 00000000..97827fa7 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_screen + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_screen](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_screen) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_size.md b/mixs6/MIMARKS_specimen_lib_size.md new file mode 100644 index 00000000..69a117c9 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_size + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_size](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_size) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_vector.md b/mixs6/MIMARKS_specimen_lib_vector.md new file mode 100644 index 00000000..a021f543 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_vector + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_vector](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_vector) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_mid.md b/mixs6/MIMARKS_specimen_mid.md new file mode 100644 index 00000000..8f3305fe --- /dev/null +++ b/mixs6/MIMARKS_specimen_mid.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_mid + + + + +URI: [mixs.vocab:MIMARKS_specimen_mid](https://w3id.org/mixs/vocab/MIMARKS_specimen_mid) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_nucl_acid_amp.md b/mixs6/MIMARKS_specimen_nucl_acid_amp.md new file mode 100644 index 00000000..6e4c13c6 --- /dev/null +++ b/mixs6/MIMARKS_specimen_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_nucl_acid_amp + + + + +URI: [mixs.vocab:MIMARKS_specimen_nucl_acid_amp](https://w3id.org/mixs/vocab/MIMARKS_specimen_nucl_acid_amp) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_nucl_acid_ext.md b/mixs6/MIMARKS_specimen_nucl_acid_ext.md new file mode 100644 index 00000000..071bc984 --- /dev/null +++ b/mixs6/MIMARKS_specimen_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_nucl_acid_ext + + + + +URI: [mixs.vocab:MIMARKS_specimen_nucl_acid_ext](https://w3id.org/mixs/vocab/MIMARKS_specimen_nucl_acid_ext) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_pcr_cond.md b/mixs6/MIMARKS_specimen_pcr_cond.md new file mode 100644 index 00000000..cb5665e0 --- /dev/null +++ b/mixs6/MIMARKS_specimen_pcr_cond.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_pcr_cond + + + + +URI: [mixs.vocab:MIMARKS_specimen_pcr_cond](https://w3id.org/mixs/vocab/MIMARKS_specimen_pcr_cond) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_cond](pcr_cond.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_pcr_primers.md b/mixs6/MIMARKS_specimen_pcr_primers.md new file mode 100644 index 00000000..5d380eac --- /dev/null +++ b/mixs6/MIMARKS_specimen_pcr_primers.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_pcr_primers + + + + +URI: [mixs.vocab:MIMARKS_specimen_pcr_primers](https://w3id.org/mixs/vocab/MIMARKS_specimen_pcr_primers) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_primers](pcr_primers.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_project_name.md b/mixs6/MIMARKS_specimen_project_name.md new file mode 100644 index 00000000..51f918f2 --- /dev/null +++ b/mixs6/MIMARKS_specimen_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_project_name + + + + +URI: [mixs.vocab:MIMARKS_specimen_project_name](https://w3id.org/mixs/vocab/MIMARKS_specimen_project_name) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_rel_to_oxygen.md b/mixs6/MIMARKS_specimen_rel_to_oxygen.md new file mode 100644 index 00000000..2a820aa3 --- /dev/null +++ b/mixs6/MIMARKS_specimen_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_rel_to_oxygen + + + + +URI: [mixs.vocab:MIMARKS_specimen_rel_to_oxygen](https://w3id.org/mixs/vocab/MIMARKS_specimen_rel_to_oxygen) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_samp_mat_process.md b/mixs6/MIMARKS_specimen_samp_mat_process.md new file mode 100644 index 00000000..54438c74 --- /dev/null +++ b/mixs6/MIMARKS_specimen_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_samp_mat_process + + + + +URI: [mixs.vocab:MIMARKS_specimen_samp_mat_process](https://w3id.org/mixs/vocab/MIMARKS_specimen_samp_mat_process) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_samp_size.md b/mixs6/MIMARKS_specimen_samp_size.md new file mode 100644 index 00000000..6f0635fe --- /dev/null +++ b/mixs6/MIMARKS_specimen_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_samp_size + + + + +URI: [mixs.vocab:MIMARKS_specimen_samp_size](https://w3id.org/mixs/vocab/MIMARKS_specimen_samp_size) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_sample_collect_device.md b/mixs6/MIMARKS_specimen_sample_collect_device.md new file mode 100644 index 00000000..e484264e --- /dev/null +++ b/mixs6/MIMARKS_specimen_sample_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_sample_collect_device + + + + +URI: [mixs.vocab:MIMARKS_specimen_sample_collect_device](https://w3id.org/mixs/vocab/MIMARKS_specimen_sample_collect_device) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_sample_collect_method.md b/mixs6/MIMARKS_specimen_sample_collect_method.md new file mode 100644 index 00000000..0596f7bc --- /dev/null +++ b/mixs6/MIMARKS_specimen_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_sample_collect_method + + + + +URI: [mixs.vocab:MIMARKS_specimen_sample_collect_method](https://w3id.org/mixs/vocab/MIMARKS_specimen_sample_collect_method) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_sample_name.md b/mixs6/MIMARKS_specimen_sample_name.md new file mode 100644 index 00000000..df5f4364 --- /dev/null +++ b/mixs6/MIMARKS_specimen_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_sample_name + + + + +URI: [mixs.vocab:MIMARKS_specimen_sample_name](https://w3id.org/mixs/vocab/MIMARKS_specimen_sample_name) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_seq_meth.md b/mixs6/MIMARKS_specimen_seq_meth.md new file mode 100644 index 00000000..9dea6c77 --- /dev/null +++ b/mixs6/MIMARKS_specimen_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_seq_meth + + + + +URI: [mixs.vocab:MIMARKS_specimen_seq_meth](https://w3id.org/mixs/vocab/MIMARKS_specimen_seq_meth) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_seq_quality_check.md b/mixs6/MIMARKS_specimen_seq_quality_check.md new file mode 100644 index 00000000..7858d202 --- /dev/null +++ b/mixs6/MIMARKS_specimen_seq_quality_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_seq_quality_check + + + + +URI: [mixs.vocab:MIMARKS_specimen_seq_quality_check](https://w3id.org/mixs/vocab/MIMARKS_specimen_seq_quality_check) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [seq_quality_check](seq_quality_check.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_size_frac.md b/mixs6/MIMARKS_specimen_size_frac.md new file mode 100644 index 00000000..08816f8c --- /dev/null +++ b/mixs6/MIMARKS_specimen_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_size_frac + + + + +URI: [mixs.vocab:MIMARKS_specimen_size_frac](https://w3id.org/mixs/vocab/MIMARKS_specimen_size_frac) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_sop.md b/mixs6/MIMARKS_specimen_sop.md new file mode 100644 index 00000000..a0a924d0 --- /dev/null +++ b/mixs6/MIMARKS_specimen_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_sop + + + + +URI: [mixs.vocab:MIMARKS_specimen_sop](https://w3id.org/mixs/vocab/MIMARKS_specimen_sop) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_source_mat_id.md b/mixs6/MIMARKS_specimen_source_mat_id.md new file mode 100644 index 00000000..db142343 --- /dev/null +++ b/mixs6/MIMARKS_specimen_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_source_mat_id + + + + +URI: [mixs.vocab:MIMARKS_specimen_source_mat_id](https://w3id.org/mixs/vocab/MIMARKS_specimen_source_mat_id) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_submitted_to_insdc.md b/mixs6/MIMARKS_specimen_submitted_to_insdc.md new file mode 100644 index 00000000..563e452f --- /dev/null +++ b/mixs6/MIMARKS_specimen_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_submitted_to_insdc + + + + +URI: [mixs.vocab:MIMARKS_specimen_submitted_to_insdc](https://w3id.org/mixs/vocab/MIMARKS_specimen_submitted_to_insdc) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_target_gene.md b/mixs6/MIMARKS_specimen_target_gene.md new file mode 100644 index 00000000..b016be2f --- /dev/null +++ b/mixs6/MIMARKS_specimen_target_gene.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_target_gene + + + + +URI: [mixs.vocab:MIMARKS_specimen_target_gene](https://w3id.org/mixs/vocab/MIMARKS_specimen_target_gene) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [target_gene](target_gene.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_target_subfragment.md b/mixs6/MIMARKS_specimen_target_subfragment.md new file mode 100644 index 00000000..e11cc820 --- /dev/null +++ b/mixs6/MIMARKS_specimen_target_subfragment.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_target_subfragment + + + + +URI: [mixs.vocab:MIMARKS_specimen_target_subfragment](https://w3id.org/mixs/vocab/MIMARKS_specimen_target_subfragment) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [target_subfragment](target_subfragment.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_url.md b/mixs6/MIMARKS_specimen_url.md new file mode 100644 index 00000000..dbe54533 --- /dev/null +++ b/mixs6/MIMARKS_specimen_url.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_url + + + + +URI: [mixs.vocab:MIMARKS_specimen_url](https://w3id.org/mixs/vocab/MIMARKS_specimen_url) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_biotic_relationship.md b/mixs6/MIMARKS_survey_biotic_relationship.md new file mode 100644 index 00000000..0febaad8 --- /dev/null +++ b/mixs6/MIMARKS_survey_biotic_relationship.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_biotic_relationship + + + + +URI: [mixs.vocab:MIMARKS_survey_biotic_relationship](https://w3id.org/mixs/vocab/MIMARKS_survey_biotic_relationship) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_chimera_check.md b/mixs6/MIMARKS_survey_chimera_check.md new file mode 100644 index 00000000..f6092ed8 --- /dev/null +++ b/mixs6/MIMARKS_survey_chimera_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_chimera_check + + + + +URI: [mixs.vocab:MIMARKS_survey_chimera_check](https://w3id.org/mixs/vocab/MIMARKS_survey_chimera_check) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [chimera_check](chimera_check.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_collection_date.md b/mixs6/MIMARKS_survey_collection_date.md new file mode 100644 index 00000000..89300003 --- /dev/null +++ b/mixs6/MIMARKS_survey_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_collection_date + + + + +URI: [mixs.vocab:MIMARKS_survey_collection_date](https://w3id.org/mixs/vocab/MIMARKS_survey_collection_date) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_broad_scale.md b/mixs6/MIMARKS_survey_env_broad_scale.md new file mode 100644 index 00000000..ed5abfe3 --- /dev/null +++ b/mixs6/MIMARKS_survey_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_env_broad_scale + + + + +URI: [mixs.vocab:MIMARKS_survey_env_broad_scale](https://w3id.org/mixs/vocab/MIMARKS_survey_env_broad_scale) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_local_scale.md b/mixs6/MIMARKS_survey_env_local_scale.md new file mode 100644 index 00000000..39d14057 --- /dev/null +++ b/mixs6/MIMARKS_survey_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_env_local_scale + + + + +URI: [mixs.vocab:MIMARKS_survey_env_local_scale](https://w3id.org/mixs/vocab/MIMARKS_survey_env_local_scale) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_medium.md b/mixs6/MIMARKS_survey_env_medium.md new file mode 100644 index 00000000..ccf19d8f --- /dev/null +++ b/mixs6/MIMARKS_survey_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_env_medium + + + + +URI: [mixs.vocab:MIMARKS_survey_env_medium](https://w3id.org/mixs/vocab/MIMARKS_survey_env_medium) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_package.md b/mixs6/MIMARKS_survey_env_package.md new file mode 100644 index 00000000..8a4f6994 --- /dev/null +++ b/mixs6/MIMARKS_survey_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_env_package + + + + +URI: [mixs.vocab:MIMARKS_survey_env_package](https://w3id.org/mixs/vocab/MIMARKS_survey_env_package) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_experimental_factor.md b/mixs6/MIMARKS_survey_experimental_factor.md new file mode 100644 index 00000000..bab276a7 --- /dev/null +++ b/mixs6/MIMARKS_survey_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_experimental_factor + + + + +URI: [mixs.vocab:MIMARKS_survey_experimental_factor](https://w3id.org/mixs/vocab/MIMARKS_survey_experimental_factor) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_extrachrom_elements.md b/mixs6/MIMARKS_survey_extrachrom_elements.md new file mode 100644 index 00000000..838655ef --- /dev/null +++ b/mixs6/MIMARKS_survey_extrachrom_elements.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_extrachrom_elements + + + + +URI: [mixs.vocab:MIMARKS_survey_extrachrom_elements](https://w3id.org/mixs/vocab/MIMARKS_survey_extrachrom_elements) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_geo_loc_name.md b/mixs6/MIMARKS_survey_geo_loc_name.md new file mode 100644 index 00000000..7b1527c4 --- /dev/null +++ b/mixs6/MIMARKS_survey_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_geo_loc_name + + + + +URI: [mixs.vocab:MIMARKS_survey_geo_loc_name](https://w3id.org/mixs/vocab/MIMARKS_survey_geo_loc_name) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_investigation_type.md b/mixs6/MIMARKS_survey_investigation_type.md new file mode 100644 index 00000000..1d7bfd38 --- /dev/null +++ b/mixs6/MIMARKS_survey_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_investigation_type + + + + +URI: [mixs.vocab:MIMARKS_survey_investigation_type](https://w3id.org/mixs/vocab/MIMARKS_survey_investigation_type) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_isol_growth_condt.md b/mixs6/MIMARKS_survey_isol_growth_condt.md new file mode 100644 index 00000000..49b2df15 --- /dev/null +++ b/mixs6/MIMARKS_survey_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_isol_growth_condt + + + + +URI: [mixs.vocab:MIMARKS_survey_isol_growth_condt](https://w3id.org/mixs/vocab/MIMARKS_survey_isol_growth_condt) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_lat_lon.md b/mixs6/MIMARKS_survey_lat_lon.md new file mode 100644 index 00000000..46d28048 --- /dev/null +++ b/mixs6/MIMARKS_survey_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_lat_lon + + + + +URI: [mixs.vocab:MIMARKS_survey_lat_lon](https://w3id.org/mixs/vocab/MIMARKS_survey_lat_lon) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_nucl_acid_amp.md b/mixs6/MIMARKS_survey_nucl_acid_amp.md new file mode 100644 index 00000000..1caecc81 --- /dev/null +++ b/mixs6/MIMARKS_survey_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_nucl_acid_amp + + + + +URI: [mixs.vocab:MIMARKS_survey_nucl_acid_amp](https://w3id.org/mixs/vocab/MIMARKS_survey_nucl_acid_amp) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_nucl_acid_ext.md b/mixs6/MIMARKS_survey_nucl_acid_ext.md new file mode 100644 index 00000000..fae56842 --- /dev/null +++ b/mixs6/MIMARKS_survey_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_nucl_acid_ext + + + + +URI: [mixs.vocab:MIMARKS_survey_nucl_acid_ext](https://w3id.org/mixs/vocab/MIMARKS_survey_nucl_acid_ext) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_pcr_cond.md b/mixs6/MIMARKS_survey_pcr_cond.md new file mode 100644 index 00000000..7bb15154 --- /dev/null +++ b/mixs6/MIMARKS_survey_pcr_cond.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_pcr_cond + + + + +URI: [mixs.vocab:MIMARKS_survey_pcr_cond](https://w3id.org/mixs/vocab/MIMARKS_survey_pcr_cond) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_cond](pcr_cond.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_pcr_primers.md b/mixs6/MIMARKS_survey_pcr_primers.md new file mode 100644 index 00000000..be85620d --- /dev/null +++ b/mixs6/MIMARKS_survey_pcr_primers.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_pcr_primers + + + + +URI: [mixs.vocab:MIMARKS_survey_pcr_primers](https://w3id.org/mixs/vocab/MIMARKS_survey_pcr_primers) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_primers](pcr_primers.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_project_name.md b/mixs6/MIMARKS_survey_project_name.md new file mode 100644 index 00000000..9b59e331 --- /dev/null +++ b/mixs6/MIMARKS_survey_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_project_name + + + + +URI: [mixs.vocab:MIMARKS_survey_project_name](https://w3id.org/mixs/vocab/MIMARKS_survey_project_name) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_rel_to_oxygen.md b/mixs6/MIMARKS_survey_rel_to_oxygen.md new file mode 100644 index 00000000..d0aa8549 --- /dev/null +++ b/mixs6/MIMARKS_survey_rel_to_oxygen.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_rel_to_oxygen + + + + +URI: [mixs.vocab:MIMARKS_survey_rel_to_oxygen](https://w3id.org/mixs/vocab/MIMARKS_survey_rel_to_oxygen) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_samp_mat_process.md b/mixs6/MIMARKS_survey_samp_mat_process.md new file mode 100644 index 00000000..858b9b0c --- /dev/null +++ b/mixs6/MIMARKS_survey_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_samp_mat_process + + + + +URI: [mixs.vocab:MIMARKS_survey_samp_mat_process](https://w3id.org/mixs/vocab/MIMARKS_survey_samp_mat_process) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_samp_size.md b/mixs6/MIMARKS_survey_samp_size.md new file mode 100644 index 00000000..de41696a --- /dev/null +++ b/mixs6/MIMARKS_survey_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_samp_size + + + + +URI: [mixs.vocab:MIMARKS_survey_samp_size](https://w3id.org/mixs/vocab/MIMARKS_survey_samp_size) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_sample_collect_device.md b/mixs6/MIMARKS_survey_sample_collect_device.md new file mode 100644 index 00000000..724689ed --- /dev/null +++ b/mixs6/MIMARKS_survey_sample_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_sample_collect_device + + + + +URI: [mixs.vocab:MIMARKS_survey_sample_collect_device](https://w3id.org/mixs/vocab/MIMARKS_survey_sample_collect_device) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_sample_collect_method.md b/mixs6/MIMARKS_survey_sample_collect_method.md new file mode 100644 index 00000000..1d02ffaf --- /dev/null +++ b/mixs6/MIMARKS_survey_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_sample_collect_method + + + + +URI: [mixs.vocab:MIMARKS_survey_sample_collect_method](https://w3id.org/mixs/vocab/MIMARKS_survey_sample_collect_method) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_sample_name.md b/mixs6/MIMARKS_survey_sample_name.md new file mode 100644 index 00000000..f54c0368 --- /dev/null +++ b/mixs6/MIMARKS_survey_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_sample_name + + + + +URI: [mixs.vocab:MIMARKS_survey_sample_name](https://w3id.org/mixs/vocab/MIMARKS_survey_sample_name) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_seq_meth.md b/mixs6/MIMARKS_survey_seq_meth.md new file mode 100644 index 00000000..659551ad --- /dev/null +++ b/mixs6/MIMARKS_survey_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_seq_meth + + + + +URI: [mixs.vocab:MIMARKS_survey_seq_meth](https://w3id.org/mixs/vocab/MIMARKS_survey_seq_meth) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_seq_quality_check.md b/mixs6/MIMARKS_survey_seq_quality_check.md new file mode 100644 index 00000000..542b5528 --- /dev/null +++ b/mixs6/MIMARKS_survey_seq_quality_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_seq_quality_check + + + + +URI: [mixs.vocab:MIMARKS_survey_seq_quality_check](https://w3id.org/mixs/vocab/MIMARKS_survey_seq_quality_check) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [seq_quality_check](seq_quality_check.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_sop.md b/mixs6/MIMARKS_survey_sop.md new file mode 100644 index 00000000..b2f4940b --- /dev/null +++ b/mixs6/MIMARKS_survey_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_sop + + + + +URI: [mixs.vocab:MIMARKS_survey_sop](https://w3id.org/mixs/vocab/MIMARKS_survey_sop) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_source_mat_id.md b/mixs6/MIMARKS_survey_source_mat_id.md new file mode 100644 index 00000000..1834bf59 --- /dev/null +++ b/mixs6/MIMARKS_survey_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_source_mat_id + + + + +URI: [mixs.vocab:MIMARKS_survey_source_mat_id](https://w3id.org/mixs/vocab/MIMARKS_survey_source_mat_id) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_submitted_to_insdc.md b/mixs6/MIMARKS_survey_submitted_to_insdc.md new file mode 100644 index 00000000..0055ba23 --- /dev/null +++ b/mixs6/MIMARKS_survey_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_submitted_to_insdc + + + + +URI: [mixs.vocab:MIMARKS_survey_submitted_to_insdc](https://w3id.org/mixs/vocab/MIMARKS_survey_submitted_to_insdc) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_subspecf_gen_lin.md b/mixs6/MIMARKS_survey_subspecf_gen_lin.md new file mode 100644 index 00000000..9dc0f40b --- /dev/null +++ b/mixs6/MIMARKS_survey_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIMARKS_survey_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIMARKS_survey_subspecf_gen_lin) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_target_gene.md b/mixs6/MIMARKS_survey_target_gene.md new file mode 100644 index 00000000..f860e4f6 --- /dev/null +++ b/mixs6/MIMARKS_survey_target_gene.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_target_gene + + + + +URI: [mixs.vocab:MIMARKS_survey_target_gene](https://w3id.org/mixs/vocab/MIMARKS_survey_target_gene) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [target_gene](target_gene.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_target_subfragment.md b/mixs6/MIMARKS_survey_target_subfragment.md new file mode 100644 index 00000000..47519379 --- /dev/null +++ b/mixs6/MIMARKS_survey_target_subfragment.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_target_subfragment + + + + +URI: [mixs.vocab:MIMARKS_survey_target_subfragment](https://w3id.org/mixs/vocab/MIMARKS_survey_target_subfragment) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [target_subfragment](target_subfragment.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_trophic_level.md b/mixs6/MIMARKS_survey_trophic_level.md new file mode 100644 index 00000000..36471f6f --- /dev/null +++ b/mixs6/MIMARKS_survey_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_trophic_level + + + + +URI: [mixs.vocab:MIMARKS_survey_trophic_level](https://w3id.org/mixs/vocab/MIMARKS_survey_trophic_level) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_url.md b/mixs6/MIMARKS_survey_url.md new file mode 100644 index 00000000..09130744 --- /dev/null +++ b/mixs6/MIMARKS_survey_url.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_url + + + + +URI: [mixs.vocab:MIMARKS_survey_url](https://w3id.org/mixs/vocab/MIMARKS_survey_url) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MISAG_sample_collect_device.md b/mixs6/MISAG_sample_collect_device.md new file mode 100644 index 00000000..f976e5ad --- /dev/null +++ b/mixs6/MISAG_sample_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_sample_collect_device + + + + +URI: [mixs.vocab:MISAG_sample_collect_device](https://w3id.org/mixs/vocab/MISAG_sample_collect_device) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MISAG_sample_collect_method.md b/mixs6/MISAG_sample_collect_method.md new file mode 100644 index 00000000..27bc27aa --- /dev/null +++ b/mixs6/MISAG_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_sample_collect_method + + + + +URI: [mixs.vocab:MISAG_sample_collect_method](https://w3id.org/mixs/vocab/MISAG_sample_collect_method) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIUVIG_sample_collect_device.md b/mixs6/MIUVIG_sample_collect_device.md new file mode 100644 index 00000000..56d0cbc3 --- /dev/null +++ b/mixs6/MIUVIG_sample_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sample_collect_device + + + + +URI: [mixs.vocab:MIUVIG_sample_collect_device](https://w3id.org/mixs/vocab/MIUVIG_sample_collect_device) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_device](sample_collect_device.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIUVIG_sample_collect_method.md b/mixs6/MIUVIG_sample_collect_method.md new file mode 100644 index 00000000..c4828d8d --- /dev/null +++ b/mixs6/MIUVIG_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sample_collect_method + + + + +URI: [mixs.vocab:MIUVIG_sample_collect_method](https://w3id.org/mixs/vocab/MIUVIG_sample_collect_method) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MagCovSoftwareEnum.md b/mixs6/MagCovSoftwareEnum.md new file mode 100644 index 00000000..fac2da39 --- /dev/null +++ b/mixs6/MagCovSoftwareEnum.md @@ -0,0 +1,19 @@ + +# Enum: mag_cov_software_enum + + + + +URI: [mixs.vocab:mag_cov_software_enum](https://w3id.org/mixs/vocab/mag_cov_software_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Me.md b/mixs6/Me.md new file mode 100644 index 00000000..22e4f75b --- /dev/null +++ b/mixs6/Me.md @@ -0,0 +1,128 @@ + +# Class: ME + + +Metagenome or Environmental + +URI: [mixs.vocab:ME](https://w3id.org/mixs/vocab/ME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][ME],[WastewaterSludgeME]uses%20-.->[ME],[SoilME]uses%20-.->[ME],[SedimentME]uses%20-.->[ME],[Plant-associatedME]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironmentME]uses%20-.->[ME],[MicrobialMatBiofilmME]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabsME]uses%20-.->[ME],[HydrocarbonResources-coresME]uses%20-.->[ME],[Human-vaginalME]uses%20-.->[ME],[Human-skinME]uses%20-.->[ME],[Human-oralME]uses%20-.->[ME],[Human-gutME]uses%20-.->[ME],[Human-associatedME]uses%20-.->[ME],[Host-associatedME]uses%20-.->[ME],[BuiltEnvironmentME]uses%20-.->[ME],[AirME]uses%20-.->[ME],[WaterME],[WastewaterSludgeME],[SoilME],[SedimentME],[Plant-associatedME],[MiscellaneousNaturalOrArtificialEnvironmentME],[MicrobialMatBiofilmME],[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-coresME],[Human-vaginalME],[Human-skinME],[Human-oralME],[Human-gutME],[Human-associatedME],[Host-associatedME],[BuiltEnvironmentME],[AirME]) + +## Mixin for + + * [AirME](AirME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package air + * [BuiltEnvironmentME](BuiltEnvironmentME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package built environment + * [Host-associatedME](Host-associatedME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package host-associated + * [Human-associatedME](Human-associatedME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-associated + * [Human-gutME](Human-gutME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-gut + * [Human-oralME](Human-oralME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-oral + * [Human-skinME](Human-skinME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-skin + * [Human-vaginalME](Human-vaginalME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-vaginal + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package miscellaneous natural or artificial environment + * [Plant-associatedME](Plant-associatedME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package plant-associated + * [SedimentME](SedimentME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package sediment + * [SoilME](SoilME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package soil + * [WastewaterSludgeME](WastewaterSludgeME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package wastewater_sludge + * [WaterME](WaterME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + * [ME➞collection_date](ME_collection_date.md) REQ + * range: [Date](types/Date.md) + * [ME➞env_broad_scale](ME_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [ME➞env_local_scale](ME_env_local_scale.md) REQ + * range: [String](types/String.md) + * [ME➞env_medium](ME_env_medium.md) REQ + * range: [String](types/String.md) + * [ME➞env_package](ME_env_package.md) OPT + * range: + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + * [ME➞geo_loc_name](ME_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + * [ME➞lat_lon](ME_lat_lon.md) REQ + * range: [String](types/String.md) + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ME | + diff --git a/mixs6/MechStrucEnum.md b/mixs6/MechStrucEnum.md new file mode 100644 index 00000000..e68f8427 --- /dev/null +++ b/mixs6/MechStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: mech_struc_enum + + + + +URI: [mixs.vocab:mech_struc_enum](https://w3id.org/mixs/vocab/mech_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/MicrobialMatBiofilm.md b/mixs6/MicrobialMatBiofilm.md new file mode 100644 index 00000000..5ec0fe7d --- /dev/null +++ b/mixs6/MicrobialMatBiofilm.md @@ -0,0 +1,309 @@ + +# Class: MicrobialMatBiofilm + + +microbial mat/biofilm + +URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBiofilm) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIUVIG],[MicrobialMatBiofilmMISAG],[MicrobialMatBiofilmMIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSpecimen],[MicrobialMatBiofilmMIMAG],[MicrobialMatBiofilmMIGSVirus],[MicrobialMatBiofilmMIGSPlant],[MicrobialMatBiofilmMIGSOrg],[MicrobialMatBiofilmMIGSEukaryote],[MicrobialMatBiofilmMIGSBacteria],[MicrobialMatBiofilmME],[QuantityValue]OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMIGSBacteria.md b/mixs6/MicrobialMatBiofilmMIGSBacteria.md new file mode 100644 index 00000000..c79f39f6 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIGSBacteria.md @@ -0,0 +1,540 @@ + +# Class: MicrobialMatBiofilmMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSBacteria](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSBacteria],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSBacteria],[MicrobialMatBiofilm],[MIGSBacteria]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIGSEukaryote.md b/mixs6/MicrobialMatBiofilmMIGSEukaryote.md new file mode 100644 index 00000000..5467b332 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIGSEukaryote.md @@ -0,0 +1,540 @@ + +# Class: MicrobialMatBiofilmMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSEukaryote](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSEukaryote],[MicrobialMatBiofilm],[MIGSEukaryote]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIGSPlant.md b/mixs6/MicrobialMatBiofilmMIGSPlant.md new file mode 100644 index 00000000..7b65f843 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIGSPlant.md @@ -0,0 +1,510 @@ + +# Class: MicrobialMatBiofilmMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSPlant](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSPlant],[MicrobialMatBiofilm],[MIGSPlant]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIGSVirus.md b/mixs6/MicrobialMatBiofilmMIGSVirus.md new file mode 100644 index 00000000..6a3b87f4 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIGSVirus.md @@ -0,0 +1,535 @@ + +# Class: MicrobialMatBiofilmMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSVirus](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSVirus],[MicrobialMatBiofilm],[MIGSVirus]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md b/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md new file mode 100644 index 00000000..c229462d --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md @@ -0,0 +1,460 @@ + +# Class: MicrobialMatBiofilmMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSpecimen](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSpecimen],[MicrobialMatBiofilm],[MIMARKSSpecimen]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md b/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md new file mode 100644 index 00000000..ff07e96a --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md @@ -0,0 +1,440 @@ + +# Class: MicrobialMatBiofilmMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSurvey](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSurvey],[MicrobialMatBiofilm],[MIMARKSSurvey]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMe.md b/mixs6/MicrobialMatBiofilmMe.md new file mode 100644 index 00000000..4627bc31 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMe.md @@ -0,0 +1,475 @@ + +# Class: MicrobialMatBiofilmME + + +Combinatorial checklist Metagenome or Environmental with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmME](https://w3id.org/mixs/vocab/MicrobialMatBiofilmME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmME],[MicrobialMatBiofilm],[ME]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsOrg.md b/mixs6/MicrobialMatBiofilmMigsOrg.md new file mode 100644 index 00000000..e9f72f32 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMigsOrg.md @@ -0,0 +1,495 @@ + +# Class: MicrobialMatBiofilmMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSOrg](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSOrg],[MicrobialMatBiofilm],[MIGSOrg]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMimag.md b/mixs6/MicrobialMatBiofilmMimag.md new file mode 100644 index 00000000..45309fff --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMimag.md @@ -0,0 +1,550 @@ + +# Class: MicrobialMatBiofilmMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIMAG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMAG],[MicrobialMatBiofilm],[MIMAG]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMisag.md b/mixs6/MicrobialMatBiofilmMisag.md new file mode 100644 index 00000000..9c310e5a --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMisag.md @@ -0,0 +1,555 @@ + +# Class: MicrobialMatBiofilmMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMISAG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMISAG],[MicrobialMatBiofilm],[MISAG]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMiuvig.md b/mixs6/MicrobialMatBiofilmMiuvig.md new file mode 100644 index 00000000..e298dc9b --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMiuvig.md @@ -0,0 +1,625 @@ + +# Class: MicrobialMatBiofilmMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIUVIG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIUVIG],[MicrobialMatBiofilm],[MIUVIG]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MigsOrg.md b/mixs6/MigsOrg.md new file mode 100644 index 00000000..4474d17a --- /dev/null +++ b/mixs6/MigsOrg.md @@ -0,0 +1,136 @@ + +# Class: MIGSOrg + + +Minimal Information about a Genome Sequence: org + +URI: [mixs.vocab:MIGSOrg](https://w3id.org/mixs/vocab/MIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSOrg],[WastewaterSludgeMIGSOrg]uses%20-.->[MIGSOrg],[SoilMIGSOrg]uses%20-.->[MIGSOrg],[SedimentMIGSOrg]uses%20-.->[MIGSOrg],[Plant-associatedMIGSOrg]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[MicrobialMatBiofilmMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-coresMIGSOrg]uses%20-.->[MIGSOrg],[Human-vaginalMIGSOrg]uses%20-.->[MIGSOrg],[Human-skinMIGSOrg]uses%20-.->[MIGSOrg],[Human-oralMIGSOrg]uses%20-.->[MIGSOrg],[Human-gutMIGSOrg]uses%20-.->[MIGSOrg],[Human-associatedMIGSOrg]uses%20-.->[MIGSOrg],[Host-associatedMIGSOrg]uses%20-.->[MIGSOrg],[BuiltEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[AirMIGSOrg]uses%20-.->[MIGSOrg],[WaterMIGSOrg],[WastewaterSludgeMIGSOrg],[SoilMIGSOrg],[SedimentMIGSOrg],[Plant-associatedMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MicrobialMatBiofilmMIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-coresMIGSOrg],[Human-vaginalMIGSOrg],[Human-skinMIGSOrg],[Human-oralMIGSOrg],[Human-gutMIGSOrg],[Human-associatedMIGSOrg],[Host-associatedMIGSOrg],[BuiltEnvironmentMIGSOrg],[AirMIGSOrg]) + +## Mixin for + + * [AirMIGSOrg](AirMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package air + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package built environment + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package host-associated + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-associated + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-gut + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-oral + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-skin + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package plant-associated + * [SedimentMIGSOrg](SedimentMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package sediment + * [SoilMIGSOrg](SoilMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package soil + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package wastewater_sludge + * [WaterMIGSOrg](WaterMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS org➞collection_date](MIGS_org_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS org➞env_broad_scale](MIGS_org_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS org➞env_local_scale](MIGS_org_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS org➞env_medium](MIGS_org_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS org➞geo_loc_name](MIGS_org_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS org➞lat_lon](MIGS_org_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.org | + diff --git a/mixs6/Mimag.md b/mixs6/Mimag.md new file mode 100644 index 00000000..55defb40 --- /dev/null +++ b/mixs6/Mimag.md @@ -0,0 +1,158 @@ + +# Class: MIMAG + + +Minimum Information About a Metagenome-Assembled Genome + +URI: [mixs.vocab:MIMAG](https://w3id.org/mixs/vocab/MIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMAG],[WastewaterSludgeMIMAG]uses%20-.->[MIMAG],[SoilMIMAG]uses%20-.->[MIMAG],[SedimentMIMAG]uses%20-.->[MIMAG],[Plant-associatedMIMAG]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG]uses%20-.->[MIMAG],[MicrobialMatBiofilmMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabsMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-coresMIMAG]uses%20-.->[MIMAG],[Human-vaginalMIMAG]uses%20-.->[MIMAG],[Human-skinMIMAG]uses%20-.->[MIMAG],[Human-oralMIMAG]uses%20-.->[MIMAG],[Human-gutMIMAG]uses%20-.->[MIMAG],[Human-associatedMIMAG]uses%20-.->[MIMAG],[Host-associatedMIMAG]uses%20-.->[MIMAG],[BuiltEnvironmentMIMAG]uses%20-.->[MIMAG],[AirMIMAG]uses%20-.->[MIMAG],[WaterMIMAG],[WastewaterSludgeMIMAG],[SoilMIMAG],[SedimentMIMAG],[Plant-associatedMIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MicrobialMatBiofilmMIMAG],[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-coresMIMAG],[Human-vaginalMIMAG],[Human-skinMIMAG],[Human-oralMIMAG],[Human-gutMIMAG],[Human-associatedMIMAG],[Host-associatedMIMAG],[BuiltEnvironmentMIMAG],[AirMIMAG]) + +## Mixin for + + * [AirMIMAG](AirMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package air + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package built environment + * [Host-associatedMIMAG](Host-associatedMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package host-associated + * [Human-associatedMIMAG](Human-associatedMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-associated + * [Human-gutMIMAG](Human-gutMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-gut + * [Human-oralMIMAG](Human-oralMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-oral + * [Human-skinMIMAG](Human-skinMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-skin + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-vaginal + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package plant-associated + * [SedimentMIMAG](SedimentMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package sediment + * [SoilMIMAG](SoilMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package wastewater_sludge + * [WaterMIMAG](WaterMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + * [MIMAG➞collection_date](MIMAG_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + * [MIMAG➞env_broad_scale](MIMAG_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIMAG➞env_local_scale](MIMAG_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIMAG➞env_medium](MIMAG_env_medium.md) REQ + * range: [String](types/String.md) + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIMAG➞geo_loc_name](MIMAG_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + * [MIMAG➞lat_lon](MIMAG_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIMAG | + diff --git a/mixs6/Misag.md b/mixs6/Misag.md new file mode 100644 index 00000000..0ca75ea5 --- /dev/null +++ b/mixs6/Misag.md @@ -0,0 +1,160 @@ + +# Class: MISAG + + +Minimum Information About a Single Amplified Genome + +URI: [mixs.vocab:MISAG](https://w3id.org/mixs/vocab/MISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MISAG],[WastewaterSludgeMISAG]uses%20-.->[MISAG],[SoilMISAG]uses%20-.->[MISAG],[SedimentMISAG]uses%20-.->[MISAG],[Plant-associatedMISAG]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG]uses%20-.->[MISAG],[MicrobialMatBiofilmMISAG]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabsMISAG]uses%20-.->[MISAG],[HydrocarbonResources-coresMISAG]uses%20-.->[MISAG],[Human-vaginalMISAG]uses%20-.->[MISAG],[Human-skinMISAG]uses%20-.->[MISAG],[Human-oralMISAG]uses%20-.->[MISAG],[Human-gutMISAG]uses%20-.->[MISAG],[Human-associatedMISAG]uses%20-.->[MISAG],[Host-associatedMISAG]uses%20-.->[MISAG],[BuiltEnvironmentMISAG]uses%20-.->[MISAG],[AirMISAG]uses%20-.->[MISAG],[WaterMISAG],[WastewaterSludgeMISAG],[SoilMISAG],[SedimentMISAG],[Plant-associatedMISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MicrobialMatBiofilmMISAG],[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-coresMISAG],[Human-vaginalMISAG],[Human-skinMISAG],[Human-oralMISAG],[Human-gutMISAG],[Human-associatedMISAG],[Host-associatedMISAG],[BuiltEnvironmentMISAG],[AirMISAG]) + +## Mixin for + + * [AirMISAG](AirMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package air + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package built environment + * [Host-associatedMISAG](Host-associatedMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package host-associated + * [Human-associatedMISAG](Human-associatedMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-associated + * [Human-gutMISAG](Human-gutMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-gut + * [Human-oralMISAG](Human-oralMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-oral + * [Human-skinMISAG](Human-skinMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-skin + * [Human-vaginalMISAG](Human-vaginalMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-vaginal + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMISAG](Plant-associatedMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package plant-associated + * [SedimentMISAG](SedimentMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package sediment + * [SoilMISAG](SoilMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package soil + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package wastewater_sludge + * [WaterMISAG](WaterMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + * [MISAG➞collection_date](MISAG_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + * [MISAG➞env_broad_scale](MISAG_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MISAG➞env_local_scale](MISAG_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MISAG➞env_medium](MISAG_env_medium.md) REQ + * range: [String](types/String.md) + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + * [MISAG➞geo_loc_name](MISAG_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + * [MISAG➞lat_lon](MISAG_lat_lon.md) REQ + * range: [String](types/String.md) + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MISAG | + diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md new file mode 100644 index 00000000..a4850e21 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md @@ -0,0 +1,233 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironment + + +miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironment) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentME],[QuantityValue]OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md new file mode 100644 index 00000000..7a65287d --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md @@ -0,0 +1,464 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSBacteria]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md new file mode 100644 index 00000000..62aa6d2d --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md @@ -0,0 +1,464 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSEukaryote]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md new file mode 100644 index 00000000..df5159fa --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md @@ -0,0 +1,434 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSPlant]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md new file mode 100644 index 00000000..9a72a280 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md @@ -0,0 +1,459 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSVirus]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md new file mode 100644 index 00000000..34d8e121 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md @@ -0,0 +1,384 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSpecimen]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md new file mode 100644 index 00000000..e75cacd7 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md @@ -0,0 +1,364 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSurvey]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md new file mode 100644 index 00000000..ad7c9958 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md @@ -0,0 +1,399 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentME + + +Combinatorial checklist Metagenome or Environmental with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentME](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentME],[MiscellaneousNaturalOrArtificialEnvironment],[ME]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md new file mode 100644 index 00000000..ef122edc --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md @@ -0,0 +1,419 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSOrg]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md new file mode 100644 index 00000000..c884dbf8 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md @@ -0,0 +1,474 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMAG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MiscellaneousNaturalOrArtificialEnvironment],[MIMAG]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md new file mode 100644 index 00000000..5cca3a9e --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md @@ -0,0 +1,479 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMISAG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MiscellaneousNaturalOrArtificialEnvironment],[MISAG]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md new file mode 100644 index 00000000..a6726458 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md @@ -0,0 +1,549 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MiscellaneousNaturalOrArtificialEnvironment],[MIUVIG]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Miuvig.md b/mixs6/Miuvig.md new file mode 100644 index 00000000..0ae415e2 --- /dev/null +++ b/mixs6/Miuvig.md @@ -0,0 +1,188 @@ + +# Class: MIUVIG + + +Minimum Information About an Uncultivated Virus Genome + +URI: [mixs.vocab:MIUVIG](https://w3id.org/mixs/vocab/MIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIUVIG],[WastewaterSludgeMIUVIG]uses%20-.->[MIUVIG],[SoilMIUVIG]uses%20-.->[MIUVIG],[SedimentMIUVIG]uses%20-.->[MIUVIG],[Plant-associatedMIUVIG]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG]uses%20-.->[MIUVIG],[MicrobialMatBiofilmMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-coresMIUVIG]uses%20-.->[MIUVIG],[Human-vaginalMIUVIG]uses%20-.->[MIUVIG],[Human-skinMIUVIG]uses%20-.->[MIUVIG],[Human-oralMIUVIG]uses%20-.->[MIUVIG],[Human-gutMIUVIG]uses%20-.->[MIUVIG],[Human-associatedMIUVIG]uses%20-.->[MIUVIG],[Host-associatedMIUVIG]uses%20-.->[MIUVIG],[BuiltEnvironmentMIUVIG]uses%20-.->[MIUVIG],[AirMIUVIG]uses%20-.->[MIUVIG],[WaterMIUVIG],[WastewaterSludgeMIUVIG],[SoilMIUVIG],[SedimentMIUVIG],[Plant-associatedMIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MicrobialMatBiofilmMIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-coresMIUVIG],[Human-vaginalMIUVIG],[Human-skinMIUVIG],[Human-oralMIUVIG],[Human-gutMIUVIG],[Human-associatedMIUVIG],[Host-associatedMIUVIG],[BuiltEnvironmentMIUVIG],[AirMIUVIG]) + +## Mixin for + + * [AirMIUVIG](AirMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package air + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package built environment + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package host-associated + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-associated + * [Human-gutMIUVIG](Human-gutMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-gut + * [Human-oralMIUVIG](Human-oralMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-oral + * [Human-skinMIUVIG](Human-skinMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-skin + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-vaginal + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package plant-associated + * [SedimentMIUVIG](SedimentMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package sediment + * [SoilMIUVIG](SoilMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package soil + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package wastewater_sludge + * [WaterMIUVIG](WaterMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + * [MIUVIG➞collection_date](MIUVIG_collection_date.md) REQ + * range: [Date](types/Date.md) + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞env_broad_scale](MIUVIG_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞env_local_scale](MIUVIG_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞env_medium](MIUVIG_env_medium.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞geo_loc_name](MIUVIG_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + * [MIUVIG➞lat_lon](MIUVIG_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIUVIG | + diff --git a/mixs6/OccupDocumentEnum.md b/mixs6/OccupDocumentEnum.md new file mode 100644 index 00000000..4fd15713 --- /dev/null +++ b/mixs6/OccupDocumentEnum.md @@ -0,0 +1,19 @@ + +# Enum: occup_document_enum + + + + +URI: [mixs.vocab:occup_document_enum](https://w3id.org/mixs/vocab/occup_document_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/OrganismCountEnum.md b/mixs6/OrganismCountEnum.md new file mode 100644 index 00000000..a1aedaad --- /dev/null +++ b/mixs6/OrganismCountEnum.md @@ -0,0 +1,19 @@ + +# Enum: organism_count_enum + + + + +URI: [mixs.vocab:organism_count_enum](https://w3id.org/mixs/vocab/organism_count_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/OxyStatSampEnum.md b/mixs6/OxyStatSampEnum.md new file mode 100644 index 00000000..7194db37 --- /dev/null +++ b/mixs6/OxyStatSampEnum.md @@ -0,0 +1,19 @@ + +# Enum: oxy_stat_samp_enum + + + + +URI: [mixs.vocab:oxy_stat_samp_enum](https://w3id.org/mixs/vocab/oxy_stat_samp_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Plant-associated.md b/mixs6/Plant-associated.md new file mode 100644 index 00000000..177f773f --- /dev/null +++ b/mixs6/Plant-associated.md @@ -0,0 +1,361 @@ + +# Class: Plant-associated + + +plant-associated + +URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIUVIG],[Plant-associatedMISAG],[Plant-associatedMIMARKSSurvey],[Plant-associatedMIMARKSSpecimen],[Plant-associatedMIMAG],[Plant-associatedMIGSVirus],[Plant-associatedMIGSPlant],[Plant-associatedMIGSOrg],[Plant-associatedMIGSEukaryote],[Plant-associatedMIGSBacteria],[Plant-associatedME],[QuantityValue]OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMIGSBacteria.md b/mixs6/Plant-associatedMIGSBacteria.md new file mode 100644 index 00000000..6c048164 --- /dev/null +++ b/mixs6/Plant-associatedMIGSBacteria.md @@ -0,0 +1,588 @@ + +# Class: Plant-associatedMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant-associatedMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSBacteria],[Plant-associated]^-[Plant-associatedMIGSBacteria],[Plant-associated],[MIGSBacteria]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIGSEukaryote.md b/mixs6/Plant-associatedMIGSEukaryote.md new file mode 100644 index 00000000..dd19f16d --- /dev/null +++ b/mixs6/Plant-associatedMIGSEukaryote.md @@ -0,0 +1,588 @@ + +# Class: Plant-associatedMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plant-associatedMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Plant-associated]^-[Plant-associatedMIGSEukaryote],[Plant-associated],[MIGSEukaryote]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIGSPlant.md b/mixs6/Plant-associatedMIGSPlant.md new file mode 100644 index 00000000..7830fc06 --- /dev/null +++ b/mixs6/Plant-associatedMIGSPlant.md @@ -0,0 +1,558 @@ + +# Class: Plant-associatedMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-associatedMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSPlant],[Plant-associated]^-[Plant-associatedMIGSPlant],[Plant-associated],[MIGSPlant]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIGSVirus.md b/mixs6/Plant-associatedMIGSVirus.md new file mode 100644 index 00000000..a7541c8d --- /dev/null +++ b/mixs6/Plant-associatedMIGSVirus.md @@ -0,0 +1,583 @@ + +# Class: Plant-associatedMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-associatedMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSVirus],[Plant-associated]^-[Plant-associatedMIGSVirus],[Plant-associated],[MIGSVirus]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Plant-associatedMIMARKSSpecimen.md b/mixs6/Plant-associatedMIMARKSSpecimen.md new file mode 100644 index 00000000..6dfb4da1 --- /dev/null +++ b/mixs6/Plant-associatedMIMARKSSpecimen.md @@ -0,0 +1,508 @@ + +# Class: Plant-associatedMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Plant-associatedMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Plant-associated]^-[Plant-associatedMIMARKSSpecimen],[Plant-associated],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIMARKSSurvey.md b/mixs6/Plant-associatedMIMARKSSurvey.md new file mode 100644 index 00000000..cae69306 --- /dev/null +++ b/mixs6/Plant-associatedMIMARKSSurvey.md @@ -0,0 +1,488 @@ + +# Class: Plant-associatedMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plant-associatedMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Plant-associated]^-[Plant-associatedMIMARKSSurvey],[Plant-associated],[MIMARKSSurvey]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMe.md b/mixs6/Plant-associatedMe.md new file mode 100644 index 00000000..92025096 --- /dev/null +++ b/mixs6/Plant-associatedMe.md @@ -0,0 +1,523 @@ + +# Class: Plant-associatedME + + +Combinatorial checklist Metagenome or Environmental with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associatedME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[ME],[Plant-associated]^-[Plant-associatedME],[Plant-associated],[ME]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsOrg.md b/mixs6/Plant-associatedMigsOrg.md new file mode 100644 index 00000000..1e41adc1 --- /dev/null +++ b/mixs6/Plant-associatedMigsOrg.md @@ -0,0 +1,543 @@ + +# Class: Plant-associatedMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-associatedMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSOrg],[Plant-associated]^-[Plant-associatedMIGSOrg],[Plant-associated],[MIGSOrg]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMimag.md b/mixs6/Plant-associatedMimag.md new file mode 100644 index 00000000..c524f740 --- /dev/null +++ b/mixs6/Plant-associatedMimag.md @@ -0,0 +1,598 @@ + +# Class: Plant-associatedMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associatedMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIMAG],[Plant-associated]^-[Plant-associatedMIMAG],[Plant-associated],[MIMAG]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMisag.md b/mixs6/Plant-associatedMisag.md new file mode 100644 index 00000000..351af4f4 --- /dev/null +++ b/mixs6/Plant-associatedMisag.md @@ -0,0 +1,603 @@ + +# Class: Plant-associatedMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associatedMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MISAG],[Plant-associated]^-[Plant-associatedMISAG],[Plant-associated],[MISAG]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMiuvig.md b/mixs6/Plant-associatedMiuvig.md new file mode 100644 index 00000000..31caac74 --- /dev/null +++ b/mixs6/Plant-associatedMiuvig.md @@ -0,0 +1,673 @@ + +# Class: Plant-associatedMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-associatedMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIUVIG],[Plant-associated]^-[Plant-associatedMIUVIG],[Plant-associated],[MIUVIG]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification. + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/PlantGrowthMedEnum.md b/mixs6/PlantGrowthMedEnum.md new file mode 100644 index 00000000..f11c5c35 --- /dev/null +++ b/mixs6/PlantGrowthMedEnum.md @@ -0,0 +1,19 @@ + +# Enum: plant_growth_med_enum + + + + +URI: [mixs.vocab:plant_growth_med_enum](https://w3id.org/mixs/vocab/plant_growth_med_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PlantSexEnum.md b/mixs6/PlantSexEnum.md new file mode 100644 index 00000000..95d2940a --- /dev/null +++ b/mixs6/PlantSexEnum.md @@ -0,0 +1,19 @@ + +# Enum: plant_sex_enum + + + + +URI: [mixs.vocab:plant_sex_enum](https://w3id.org/mixs/vocab/plant_sex_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PredGenomeStrucEnum.md b/mixs6/PredGenomeStrucEnum.md new file mode 100644 index 00000000..0fb044dc --- /dev/null +++ b/mixs6/PredGenomeStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: pred_genome_struc_enum + + + + +URI: [mixs.vocab:pred_genome_struc_enum](https://w3id.org/mixs/vocab/pred_genome_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PredGenomeTypeEnum.md b/mixs6/PredGenomeTypeEnum.md new file mode 100644 index 00000000..c47cf479 --- /dev/null +++ b/mixs6/PredGenomeTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: pred_genome_type_enum + + + + +URI: [mixs.vocab:pred_genome_type_enum](https://w3id.org/mixs/vocab/pred_genome_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PresAnimalEnum.md b/mixs6/PresAnimalEnum.md new file mode 100644 index 00000000..7529f727 --- /dev/null +++ b/mixs6/PresAnimalEnum.md @@ -0,0 +1,19 @@ + +# Enum: pres_animal_enum + + + + +URI: [mixs.vocab:pres_animal_enum](https://w3id.org/mixs/vocab/pres_animal_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ProfilePositionEnum.md b/mixs6/ProfilePositionEnum.md new file mode 100644 index 00000000..763d9908 --- /dev/null +++ b/mixs6/ProfilePositionEnum.md @@ -0,0 +1,19 @@ + +# Enum: profile_position_enum + + + + +URI: [mixs.vocab:profile_position_enum](https://w3id.org/mixs/vocab/profile_position_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/QuadPosEnum.md b/mixs6/QuadPosEnum.md new file mode 100644 index 00000000..0e2fb6a5 --- /dev/null +++ b/mixs6/QuadPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: quad_pos_enum + + + + +URI: [mixs.vocab:quad_pos_enum](https://w3id.org/mixs/vocab/quad_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/QuantityValue.md b/mixs6/QuantityValue.md new file mode 100644 index 00000000..5e63b60d --- /dev/null +++ b/mixs6/QuantityValue.md @@ -0,0 +1,196 @@ + +# Class: QuantityValue + + +used to record a measurement + +URI: [mixs.vocab:QuantityValue](https://w3id.org/mixs/vocab/QuantityValue) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[ME]++-%20samp_size%200..1>[QuantityValue|has_unit:string%20%3F;has_numeric_value:double%20%3F;has_raw_value:string%20%3F],[MIGSBacteria]++-%20samp_size%200..1>[QuantityValue],[MIGSEukaryote]++-%20samp_size%200..1>[QuantityValue],[MIGSOrg]++-%20samp_size%200..1>[QuantityValue],[MIGSPlant]++-%20samp_size%200..1>[QuantityValue],[MIGSVirus]++-%20samp_size%200..1>[QuantityValue],[MIMAG]++-%20samp_size%200..1>[QuantityValue],[MIMARKSSpecimen]++-%20samp_size%200..1>[QuantityValue],[MIMARKSSurvey]++-%20samp_size%200..1>[QuantityValue],[MISAG]++-%20samp_size%200..1>[QuantityValue],[MIUVIG]++-%20samp_size%200..1>[QuantityValue],[BuiltEnvironment]++-%20abs_air_humidity%200..1>[QuantityValue],[BuiltEnvironment]++-%20air_temp%200..1>[QuantityValue],[Soil]++-%20al_sat%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20alkalinity%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20alkalinity%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20alkalinity%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20alkalinity%200..1>[QuantityValue],[Sediment]++-%20alkalinity%200..1>[QuantityValue],[WastewaterSludge]++-%20alkalinity%200..1>[QuantityValue],[Water]++-%20alkalinity%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20alkyl_diethers%200..1>[QuantityValue],[Sediment]++-%20alkyl_diethers%200..1>[QuantityValue],[Water]++-%20alkyl_diethers%200..1>[QuantityValue],[Core]++-%20alt%200..1>[QuantityValue],[Air]++-%20alt%200..1>[QuantityValue],[BuiltEnvironment]++-%20alt%200..1>[QuantityValue],[Host-associated]++-%20alt%200..1>[QuantityValue],[Human-associated]++-%20alt%200..1>[QuantityValue],[Human-gut]++-%20alt%200..1>[QuantityValue],[Human-oral]++-%20alt%200..1>[QuantityValue],[Human-skin]++-%20alt%200..1>[QuantityValue],[Human-vaginal]++-%20alt%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20alt%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20alt%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20alt%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20alt%200..1>[QuantityValue],[Plant-associated]++-%20alt%200..1>[QuantityValue],[Sediment]++-%20alt%200..1>[QuantityValue],[Soil]++-%20alt%200..1>[QuantityValue],[WastewaterSludge]++-%20alt%200..1>[QuantityValue],[Water]++-%20alt%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20aminopept_act%200..1>[QuantityValue],[Sediment]++-%20aminopept_act%200..1>[QuantityValue],[Water]++-%20aminopept_act%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20ammonium%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20ammonium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20ammonium%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20ammonium%200..1>[QuantityValue],[Sediment]++-%20ammonium%200..1>[QuantityValue],[Water]++-%20ammonium%200..1>[QuantityValue],[BuiltEnvironment]++-%20amount_light%200..1>[QuantityValue],[Soil]++-%20annual_precpt%200..1>[QuantityValue],[Soil]++-%20annual_temp%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20api%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20api%200..1>[QuantityValue],[BuiltEnvironment]++-%20avg_dew_point%200..1>[QuantityValue],[BuiltEnvironment]++-%20avg_temp%200..1>[QuantityValue],[Water]++-%20bac_prod%200..1>[QuantityValue],[Water]++-%20bac_resp%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20bacteria_carb_prod%200..1>[QuantityValue],[Sediment]++-%20bacteria_carb_prod%200..1>[QuantityValue],[Water]++-%20bacteria_carb_prod%200..1>[QuantityValue],[Air]++-%20barometric_press%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20benzene%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20benzene%200..1>[QuantityValue],[WastewaterSludge]++-%20biochem_oxygen_dem%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20bishomohopanol%200..1>[QuantityValue],[Sediment]++-%20bishomohopanol%200..1>[QuantityValue],[Water]++-%20bishomohopanol%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20bromide%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20bromide%200..1>[QuantityValue],[Sediment]++-%20bromide%200..1>[QuantityValue],[Water]++-%20bromide%200..1>[QuantityValue],[BuiltEnvironment]++-%20built_struc_age%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20calcium%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20calcium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20calcium%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20calcium%200..1>[QuantityValue],[Sediment]++-%20calcium%200..1>[QuantityValue],[Water]++-%20calcium%200..1>[QuantityValue],[Air]++-%20carb_dioxide%200..1>[QuantityValue],[BuiltEnvironment]++-%20carb_dioxide%200..1>[QuantityValue],[Air]++-%20carb_monoxide%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20carb_nitro_ratio%200..1>[QuantityValue],[Sediment]++-%20carb_nitro_ratio%200..1>[QuantityValue],[Water]++-%20carb_nitro_ratio%200..1>[QuantityValue],[BuiltEnvironment]++-%20ceil_area%200..1>[QuantityValue],[BuiltEnvironment]++-%20ceil_thermal_mass%200..1>[QuantityValue],[WastewaterSludge]++-%20chem_oxygen_dem%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20chloride%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20chloride%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20chloride%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20chloride%200..1>[QuantityValue],[Sediment]++-%20chloride%200..1>[QuantityValue],[Water]++-%20chloride%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20chlorophyll%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20chlorophyll%200..1>[QuantityValue],[Sediment]++-%20chlorophyll%200..1>[QuantityValue],[Water]++-%20chlorophyll%200..1>[QuantityValue],[Water]++-%20conduc%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20density%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20density%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20density%200..1>[QuantityValue],[Sediment]++-%20density%200..1>[QuantityValue],[Water]++-%20density%200..1>[QuantityValue],[BuiltEnvironment]++-%20dew_point%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20diss_carb_dioxide%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20diss_carb_dioxide%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20diss_carb_dioxide%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20diss_carb_dioxide%200..1>[QuantityValue],[Sediment]++-%20diss_carb_dioxide%200..1>[QuantityValue],[Water]++-%20diss_carb_dioxide%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20diss_hydrogen%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20diss_hydrogen%200..1>[QuantityValue],[Sediment]++-%20diss_hydrogen%200..1>[QuantityValue],[Water]++-%20diss_hydrogen%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20diss_inorg_carb%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20diss_inorg_carb%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20diss_inorg_carb%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20diss_inorg_carb%200..1>[QuantityValue],[Sediment]++-%20diss_inorg_carb%200..1>[QuantityValue],[Water]++-%20diss_inorg_carb%200..1>[QuantityValue],[Water]++-%20diss_inorg_nitro%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20diss_inorg_phosp%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20diss_inorg_phosp%200..1>[QuantityValue],[Water]++-%20diss_inorg_phosp%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20diss_iron%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20diss_iron%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20diss_org_carb%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20diss_org_carb%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20diss_org_carb%200..1>[QuantityValue],[Sediment]++-%20diss_org_carb%200..1>[QuantityValue],[Water]++-%20diss_org_carb%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20diss_org_nitro%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20diss_org_nitro%200..1>[QuantityValue],[Sediment]++-%20diss_org_nitro%200..1>[QuantityValue],[Water]++-%20diss_org_nitro%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20diss_oxygen%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20diss_oxygen%200..1>[QuantityValue],[Sediment]++-%20diss_oxygen%200..1>[QuantityValue],[Water]++-%20diss_oxygen%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20diss_oxygen_fluid%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20diss_oxygen_fluid%200..1>[QuantityValue],[BuiltEnvironment]++-%20door_size%200..1>[QuantityValue],[Water]++-%20down_par%200..1>[QuantityValue],[WastewaterSludge]++-%20efficiency_percent%200..1>[QuantityValue],[Core]++-%20elev%200..1>[QuantityValue],[Air]++-%20elev%200..1>[QuantityValue],[BuiltEnvironment]++-%20elev%200..1>[QuantityValue],[Host-associated]++-%20elev%200..1>[QuantityValue],[Human-associated]++-%20elev%200..1>[QuantityValue],[Human-gut]++-%20elev%200..1>[QuantityValue],[Human-oral]++-%20elev%200..1>[QuantityValue],[Human-skin]++-%20elev%200..1>[QuantityValue],[Human-vaginal]++-%20elev%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20elev%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20elev%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20elev%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20elev%200..1>[QuantityValue],[Plant-associated]++-%20elev%200..1>[QuantityValue],[Sediment]++-%20elev%200..1>[QuantityValue],[Soil]++-%20elev%200..1>[QuantityValue],[WastewaterSludge]++-%20elev%200..1>[QuantityValue],[Water]++-%20elev%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20ethylbenzene%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20ethylbenzene%200..1>[QuantityValue],[BuiltEnvironment]++-%20exp_duct%200..1>[QuantityValue],[Soil]++-%20extreme_salinity%200..1>[QuantityValue],[BuiltEnvironment]++-%20floor_age%200..1>[QuantityValue],[BuiltEnvironment]++-%20floor_area%200..1>[QuantityValue],[BuiltEnvironment]++-%20floor_thermal_mass%200..1>[QuantityValue],[Water]++-%20fluor%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20glucosidase_act%200..1>[QuantityValue],[Sediment]++-%20glucosidase_act%200..1>[QuantityValue],[Water]++-%20glucosidase_act%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20hcr_fw_salinity%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20hcr_fw_salinity%200..1>[QuantityValue],[BuiltEnvironment]++-%20height_carper_fiber%200..1>[QuantityValue],[Host-associated]++-%20host_age%200..1>[QuantityValue],[Human-associated]++-%20host_age%200..1>[QuantityValue],[Human-gut]++-%20host_age%200..1>[QuantityValue],[Human-oral]++-%20host_age%200..1>[QuantityValue],[Human-skin]++-%20host_age%200..1>[QuantityValue],[Human-vaginal]++-%20host_age%200..1>[QuantityValue],[Plant-associated]++-%20host_age%200..1>[QuantityValue],[Host-associated]++-%20host_blood_press_diast%200..1>[QuantityValue],[Host-associated]++-%20host_blood_press_syst%200..1>[QuantityValue],[Human-associated]++-%20host_body_mass_index%200..1>[QuantityValue],[Human-gut]++-%20host_body_mass_index%200..1>[QuantityValue],[Human-oral]++-%20host_body_mass_index%200..1>[QuantityValue],[Human-skin]++-%20host_body_mass_index%200..1>[QuantityValue],[Human-vaginal]++-%20host_body_mass_index%200..1>[QuantityValue],[Host-associated]++-%20host_body_temp%200..1>[QuantityValue],[Human-associated]++-%20host_body_temp%200..1>[QuantityValue],[Human-gut]++-%20host_body_temp%200..1>[QuantityValue],[Human-oral]++-%20host_body_temp%200..1>[QuantityValue],[Human-skin]++-%20host_body_temp%200..1>[QuantityValue],[Human-vaginal]++-%20host_body_temp%200..1>[QuantityValue],[Host-associated]++-%20host_dry_mass%200..1>[QuantityValue],[Plant-associated]++-%20host_dry_mass%200..1>[QuantityValue],[Host-associated]++-%20host_height%200..1>[QuantityValue],[Human-associated]++-%20host_height%200..1>[QuantityValue],[Human-gut]++-%20host_height%200..1>[QuantityValue],[Human-oral]++-%20host_height%200..1>[QuantityValue],[Human-skin]++-%20host_height%200..1>[QuantityValue],[Human-vaginal]++-%20host_height%200..1>[QuantityValue],[Plant-associated]++-%20host_height%200..1>[QuantityValue],[Host-associated]++-%20host_length%200..1>[QuantityValue],[Plant-associated]++-%20host_length%200..1>[QuantityValue],[Human-associated]++-%20host_pulse%200..1>[QuantityValue],[Human-gut]++-%20host_pulse%200..1>[QuantityValue],[Human-oral]++-%20host_pulse%200..1>[QuantityValue],[Human-skin]++-%20host_pulse%200..1>[QuantityValue],[Human-vaginal]++-%20host_pulse%200..1>[QuantityValue],[Host-associated]++-%20host_tot_mass%200..1>[QuantityValue],[Human-associated]++-%20host_tot_mass%200..1>[QuantityValue],[Human-gut]++-%20host_tot_mass%200..1>[QuantityValue],[Human-oral]++-%20host_tot_mass%200..1>[QuantityValue],[Human-skin]++-%20host_tot_mass%200..1>[QuantityValue],[Human-vaginal]++-%20host_tot_mass%200..1>[QuantityValue],[Plant-associated]++-%20host_tot_mass%200..1>[QuantityValue],[Plant-associated]++-%20host_wet_mass%200..1>[QuantityValue],[Air]++-%20humidity%200..1>[QuantityValue],[WastewaterSludge]++-%20indust_eff_percent%200..1>[QuantityValue],[BuiltEnvironment]++-%20inside_lux%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20iwf%200..1>[QuantityValue],[Water]++-%20light_intensity%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20magnesium%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20magnesium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20magnesium%200..1>[QuantityValue],[Sediment]++-%20magnesium%200..1>[QuantityValue],[Water]++-%20magnesium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20mean_frict_vel%200..1>[QuantityValue],[Sediment]++-%20mean_frict_vel%200..1>[QuantityValue],[Water]++-%20mean_frict_vel%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20mean_peak_frict_vel%200..1>[QuantityValue],[Sediment]++-%20mean_peak_frict_vel%200..1>[QuantityValue],[Water]++-%20mean_peak_frict_vel%200..1>[QuantityValue],[Air]++-%20methane%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20methane%200..1>[QuantityValue],[Sediment]++-%20methane%200..1>[QuantityValue],[Soil]++-%20microbial_biomass%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20nitrate%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20nitrate%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20nitrate%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20nitrate%200..1>[QuantityValue],[Sediment]++-%20nitrate%200..1>[QuantityValue],[WastewaterSludge]++-%20nitrate%200..1>[QuantityValue],[Water]++-%20nitrate%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20nitrite%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20nitrite%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20nitrite%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20nitrite%200..1>[QuantityValue],[Sediment]++-%20nitrite%200..1>[QuantityValue],[Water]++-%20nitrite%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20nitro%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20nitro%200..1>[QuantityValue],[Sediment]++-%20nitro%200..1>[QuantityValue],[Water]++-%20nitro%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20org_carb%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20org_carb%200..1>[QuantityValue],[Sediment]++-%20org_carb%200..1>[QuantityValue],[Water]++-%20org_carb%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20org_matter%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20org_matter%200..1>[QuantityValue],[Sediment]++-%20org_matter%200..1>[QuantityValue],[Water]++-%20org_matter%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20org_nitro%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20org_nitro%200..1>[QuantityValue],[Sediment]++-%20org_nitro%200..1>[QuantityValue],[Water]++-%20org_nitro%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20owc_tvdss%200..1>[QuantityValue],[Air]++-%20oxygen%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20part_org_carb%200..1>[QuantityValue],[Sediment]++-%20part_org_carb%200..1>[QuantityValue],[Water]++-%20part_org_carb%200..1>[QuantityValue],[Water]++-%20part_org_nitro%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20petroleum_hydrocarb%200..1>[QuantityValue],[Sediment]++-%20petroleum_hydrocarb%200..1>[QuantityValue],[Water]++-%20petroleum_hydrocarb%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20phosphate%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20phosphate%200..1>[QuantityValue],[Sediment]++-%20phosphate%200..1>[QuantityValue],[WastewaterSludge]++-%20phosphate%200..1>[QuantityValue],[Water]++-%20phosphate%200..1>[QuantityValue],[Water]++-%20photon_flux%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20potassium%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20potassium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20potassium%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20potassium%200..1>[QuantityValue],[Sediment]++-%20potassium%200..1>[QuantityValue],[Water]++-%20potassium%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20pour_point%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20pour_point%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20pressure%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20pressure%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20pressure%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20pressure%200..1>[QuantityValue],[Sediment]++-%20pressure%200..1>[QuantityValue],[Water]++-%20pressure%200..1>[QuantityValue],[Water]++-%20primary_prod%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20prod_rate%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20redox_potential%200..1>[QuantityValue],[Sediment]++-%20redox_potential%200..1>[QuantityValue],[Water]++-%20redox_potential%200..1>[QuantityValue],[BuiltEnvironment]++-%20rel_air_humidity%200..1>[QuantityValue],[BuiltEnvironment]++-%20rel_humidity_out%200..1>[QuantityValue],[BuiltEnvironment]++-%20room_air_exch_rate%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20salinity%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20salinity%200..1>[QuantityValue],[Sediment]++-%20salinity%200..1>[QuantityValue],[Water]++-%20salinity%200..1>[QuantityValue],[Air]++-%20samp_salinity%200..1>[QuantityValue],[Host-associated]++-%20samp_salinity%200..1>[QuantityValue],[Human-associated]++-%20samp_salinity%200..1>[QuantityValue],[Human-gut]++-%20samp_salinity%200..1>[QuantityValue],[Human-oral]++-%20samp_salinity%200..1>[QuantityValue],[Human-skin]++-%20samp_salinity%200..1>[QuantityValue],[Human-vaginal]++-%20samp_salinity%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20samp_salinity%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20samp_salinity%200..1>[QuantityValue],[Plant-associated]++-%20samp_salinity%200..1>[QuantityValue],[WastewaterSludge]++-%20samp_salinity%200..1>[QuantityValue],[MIGSEukaryote]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSBacteria]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSPlant]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSVirus]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSOrg]++-%20samp_size(i)%200..1>[QuantityValue],[ME]++-%20samp_size(i)%200..1>[QuantityValue],[MIMARKSSpecimen]++-%20samp_size(i)%200..1>[QuantityValue],[MIMARKSSurvey]++-%20samp_size(i)%200..1>[QuantityValue],[MISAG]++-%20samp_size(i)%200..1>[QuantityValue],[MIMAG]++-%20samp_size(i)%200..1>[QuantityValue],[MIUVIG]++-%20samp_size(i)%200..1>[QuantityValue],[Core]++-%20samp_size%200..1>[QuantityValue],[Air]++-%20samp_store_temp%200..1>[QuantityValue],[Host-associated]++-%20samp_store_temp%200..1>[QuantityValue],[Human-associated]++-%20samp_store_temp%200..1>[QuantityValue],[Human-gut]++-%20samp_store_temp%200..1>[QuantityVal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+-%20temp_out%200..1>[QuantityValue],[Soil]++-%20texture%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20toluene%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20toluene%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20tot_carb%200..1>[QuantityValue],[Sediment]++-%20tot_carb%200..1>[QuantityValue],[Sediment]++-%20tot_depth_water_col%200..1>[QuantityValue],[Water]++-%20tot_depth_water_col%200..1>[QuantityValue],[Water]++-%20tot_diss_nitro%200..1>[QuantityValue],[Water]++-%20tot_inorg_nitro%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_iron%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_iron%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_nitro%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_nitro%200..1>[QuantityValue],[WastewaterSludge]++-%20tot_nitro%200..1>[QuantityValue],[Water]++-%20tot_nitro%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20tot_nitro_content%200..1>[QuantityValue],[Sediment]++-%20tot_nitro_content%200..1>[QuantityValue],[Soil]++-%20tot_nitro_content%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20tot_org_carb%200..1>[QuantityValue],[Sediment]++-%20tot_org_carb%200..1>[QuantityValue],[Soil]++-%20tot_org_carb%200..1>[QuantityValue],[Water]++-%20tot_part_carb%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_phosp%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_phosp%200..1>[QuantityValue],[Water]++-%20tot_phosp%200..1>[QuantityValue],[WastewaterSludge]++-%20tot_phosphate%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_sulfur%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_sulfur%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20turbidity%200..1>[QuantityValue],[Sediment]++-%20turbidity%200..1>[QuantityValue],[Water]++-%20turbidity%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tvdss_of_hcr_pressure%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tvdss_of_hcr_pressure%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tvdss_of_hcr_temp%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tvdss_of_hcr_temp%200..1>[QuantityValue],[Air]++-%20ventilation_rate%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20vfa%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20vfa%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20vfa_fw%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20vfa_fw%200..1>[QuantityValue],[BuiltEnvironment]++-%20wall_area%200..1>[QuantityValue],[BuiltEnvironment]++-%20wall_height%200..1>[QuantityValue],[BuiltEnvironment]++-%20wall_thermal_mass%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20water_content%200..1>[QuantityValue],[Sediment]++-%20water_content%200..1>[QuantityValue],[Soil]++-%20water_content%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20water_current%200..1>[QuantityValue],[Water]++-%20water_current%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20water_cut%200..1>[QuantityValue],[BuiltEnvironment]++-%20water_feat_size%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20water_production_rate%200..1>[QuantityValue],[Air]++-%20wind_speed%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20xylene%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20xylene%200..1>[QuantityValue],[Water],[WastewaterSludge],[Soil],[Sediment],[Plant-associated],[MiscellaneousNaturalOrArtificialEnvironment],[MicrobialMatBiofilm],[HydrocarbonResources-fluidsSwabs],[HydrocarbonResources-cores],[Human-vaginal],[Human-skin],[Human-oral],[Human-gut],[Human-associated],[Host-associated],[Core],[BuiltEnvironment],[Air],[MIUVIG],[MISAG],[MIMARKSSurvey],[MIMARKSSpecimen],[MIMAG],[MIGSVirus],[MIGSPlant],[MIGSOrg],[MIGSEukaryote],[MIGSBacteria],[ME]) + +## Referenced by class + + * **[ME](ME.md)** *[ME➞samp_size](ME_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSBacteria](MIGSBacteria.md)** *[MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSEukaryote](MIGSEukaryote.md)** *[MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSOrg](MIGSOrg.md)** *[MIGS org➞samp_size](MIGS_org_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSPlant](MIGSPlant.md)** *[MIGS plant➞samp_size](MIGS_plant_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSVirus](MIGSVirus.md)** *[MIGS virus➞samp_size](MIGS_virus_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIMAG](MIMAG.md)** *[MIMAG➞samp_size](MIMAG_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIMARKSSpecimen](MIMARKSSpecimen.md)** *[MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIMARKSSurvey](MIMARKSSurvey.md)** *[MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MISAG](MISAG.md)** *[MISAG➞samp_size](MISAG_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIUVIG](MIUVIG.md)** *[MIUVIG➞samp_size](MIUVIG_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[abs_air_humidity](abs_air_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[air_temp](air_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[al_sat](al_sat.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[alkalinity](alkalinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[alkyl_diethers](alkyl_diethers.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[alt](alt.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[aminopept_act](aminopept_act.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ammonium](ammonium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[amount_light](amount_light.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[annual_precpt](annual_precpt.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[annual_temp](annual_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[api](api.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[avg_dew_point](avg_dew_point.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[avg_temp](avg_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bac_prod](bac_prod.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bac_resp](bac_resp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bacteria_carb_prod](bacteria_carb_prod.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[barometric_press](barometric_press.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[benzene](benzene.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[biochem_oxygen_dem](biochem_oxygen_dem.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bishomohopanol](bishomohopanol.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bromide](bromide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[built_struc_age](built_struc_age.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[calcium](calcium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[carb_dioxide](carb_dioxide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[carb_monoxide](carb_monoxide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[carb_nitro_ratio](carb_nitro_ratio.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ceil_area](ceil_area.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ceil_thermal_mass](ceil_thermal_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[chem_oxygen_dem](chem_oxygen_dem.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[chloride](chloride.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[chlorophyll](chlorophyll.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[conduc](conduc.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[density](density.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[dew_point](dew_point.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_carb_dioxide](diss_carb_dioxide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_hydrogen](diss_hydrogen.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_inorg_carb](diss_inorg_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_inorg_nitro](diss_inorg_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_inorg_phosp](diss_inorg_phosp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_iron](diss_iron.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_org_carb](diss_org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_org_nitro](diss_org_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_oxygen](diss_oxygen.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_oxygen_fluid](diss_oxygen_fluid.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[door_size](door_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[down_par](down_par.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[efficiency_percent](efficiency_percent.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[elev](elev.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ethylbenzene](ethylbenzene.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[exp_duct](exp_duct.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[extreme_salinity](extreme_salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[floor_age](floor_age.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[floor_area](floor_area.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[floor_thermal_mass](floor_thermal_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[fluor](fluor.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[glucosidase_act](glucosidase_act.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[hcr_fw_salinity](hcr_fw_salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[height_carper_fiber](height_carper_fiber.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_age](host_age.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_blood_press_diast](host_blood_press_diast.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_blood_press_syst](host_blood_press_syst.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_body_mass_index](host_body_mass_index.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_body_temp](host_body_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_dry_mass](host_dry_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_height](host_height.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_length](host_length.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_pulse](host_pulse.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_tot_mass](host_tot_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_wet_mass](host_wet_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[humidity](humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[indust_eff_percent](indust_eff_percent.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[inside_lux](inside_lux.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[iwf](iwf.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[light_intensity](light_intensity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[magnesium](magnesium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[mean_frict_vel](mean_frict_vel.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[mean_peak_frict_vel](mean_peak_frict_vel.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[methane](methane.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[microbial_biomass](microbial_biomass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[nitrate](nitrate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[nitrite](nitrite.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[nitro](nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[org_carb](org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[org_matter](org_matter.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[org_nitro](org_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[owc_tvdss](owc_tvdss.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[oxygen](oxygen.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[part_org_carb](part_org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[part_org_nitro](part_org_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[petroleum_hydrocarb](petroleum_hydrocarb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[phosphate](phosphate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[photon_flux](photon_flux.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[potassium](potassium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[pour_point](pour_point.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[pressure](pressure.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[primary_prod](primary_prod.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[prod_rate](prod_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[redox_potential](redox_potential.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[rel_air_humidity](rel_air_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[rel_humidity_out](rel_humidity_out.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[room_air_exch_rate](room_air_exch_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[salinity](salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_salinity](samp_salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_size](samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_store_temp](samp_store_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_vol_we_dna_ext](samp_vol_we_dna_ext.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[season_precpt](season_precpt.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[season_temp](season_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[silicate](silicate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[size_frac_low](size_frac_low.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[size_frac_up](size_frac_up.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[slope_aspect](slope_aspect.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[slope_gradient](slope_gradient.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sludge_retent_time](sludge_retent_time.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sodium](sodium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[solar_irradiance](solar_irradiance.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[soluble_react_phosp](soluble_react_phosp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[specific_humidity](specific_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sulfate](sulfate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sulfate_fw](sulfate_fw.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sulfide](sulfide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[surf_humidity](surf_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[surf_moisture](surf_moisture.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[surf_temp](surf_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[suspend_part_matter](suspend_part_matter.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tan](tan.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[temp](temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[temp_out](temp_out.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[texture](texture.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[toluene](toluene.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_carb](tot_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_depth_water_col](tot_depth_water_col.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_diss_nitro](tot_diss_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_inorg_nitro](tot_inorg_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_iron](tot_iron.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_nitro](tot_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_nitro_content](tot_nitro_content.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_org_carb](tot_org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_part_carb](tot_part_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_phosp](tot_phosp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_phosphate](tot_phosphate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_sulfur](tot_sulfur.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[turbidity](turbidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tvdss_of_hcr_temp](tvdss_of_hcr_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ventilation_rate](ventilation_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[vfa](vfa.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[vfa_fw](vfa_fw.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wall_area](wall_area.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wall_height](wall_height.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wall_thermal_mass](wall_thermal_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_content](water_content.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_current](water_current.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_cut](water_cut.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_feat_size](water_feat_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_production_rate](water_production_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wind_speed](wind_speed.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[xylene](xylene.md)* OPT **[QuantityValue](QuantityValue.md)** + +## Attributes + + +### Own + + * [➞has numeric value](quantityValue__has_numeric_value.md) OPT + * range: [Double](types/Double.md) + * [➞has raw value](quantityValue__has_raw_value.md) OPT + * range: [String](types/String.md) + * [➞has unit](quantityValue__has_unit.md) OPT + * Description: Example "m" + * range: [String](types/String.md) diff --git a/mixs6/RelSampLocEnum.md b/mixs6/RelSampLocEnum.md new file mode 100644 index 00000000..7a40bb43 --- /dev/null +++ b/mixs6/RelSampLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: rel_samp_loc_enum + + + + +URI: [mixs.vocab:rel_samp_loc_enum](https://w3id.org/mixs/vocab/rel_samp_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RelToOxygenEnum.md b/mixs6/RelToOxygenEnum.md new file mode 100644 index 00000000..25d2e92d --- /dev/null +++ b/mixs6/RelToOxygenEnum.md @@ -0,0 +1,19 @@ + +# Enum: rel_to_oxygen_enum + + + + +URI: [mixs.vocab:rel_to_oxygen_enum](https://w3id.org/mixs/vocab/rel_to_oxygen_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomCondtEnum.md b/mixs6/RoomCondtEnum.md new file mode 100644 index 00000000..56e0d3c7 --- /dev/null +++ b/mixs6/RoomCondtEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_condt_enum + + + + +URI: [mixs.vocab:room_condt_enum](https://w3id.org/mixs/vocab/room_condt_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomConnectedEnum.md b/mixs6/RoomConnectedEnum.md new file mode 100644 index 00000000..87895180 --- /dev/null +++ b/mixs6/RoomConnectedEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_connected_enum + + + + +URI: [mixs.vocab:room_connected_enum](https://w3id.org/mixs/vocab/room_connected_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomLocEnum.md b/mixs6/RoomLocEnum.md new file mode 100644 index 00000000..73672520 --- /dev/null +++ b/mixs6/RoomLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_loc_enum + + + + +URI: [mixs.vocab:room_loc_enum](https://w3id.org/mixs/vocab/room_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomSampPosEnum.md b/mixs6/RoomSampPosEnum.md new file mode 100644 index 00000000..f486e3c1 --- /dev/null +++ b/mixs6/RoomSampPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_samp_pos_enum + + + + +URI: [mixs.vocab:room_samp_pos_enum](https://w3id.org/mixs/vocab/room_samp_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomTypeEnum.md b/mixs6/RoomTypeEnum.md new file mode 100644 index 00000000..71b1cd10 --- /dev/null +++ b/mixs6/RoomTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_type_enum + + + + +URI: [mixs.vocab:room_type_enum](https://w3id.org/mixs/vocab/room_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampCaptStatusEnum.md b/mixs6/SampCaptStatusEnum.md new file mode 100644 index 00000000..7dc54050 --- /dev/null +++ b/mixs6/SampCaptStatusEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_capt_status_enum + + + + +URI: [mixs.vocab:samp_capt_status_enum](https://w3id.org/mixs/vocab/samp_capt_status_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampCollectionPointEnum.md b/mixs6/SampCollectionPointEnum.md new file mode 100644 index 00000000..51f7de7b --- /dev/null +++ b/mixs6/SampCollectionPointEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_collection_point_enum + + + + +URI: [mixs.vocab:samp_collection_point_enum](https://w3id.org/mixs/vocab/samp_collection_point_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampDisStageEnum.md b/mixs6/SampDisStageEnum.md new file mode 100644 index 00000000..62c596f5 --- /dev/null +++ b/mixs6/SampDisStageEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_dis_stage_enum + + + + +URI: [mixs.vocab:samp_dis_stage_enum](https://w3id.org/mixs/vocab/samp_dis_stage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampFloorEnum.md b/mixs6/SampFloorEnum.md new file mode 100644 index 00000000..bc05f407 --- /dev/null +++ b/mixs6/SampFloorEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_floor_enum + + + + +URI: [mixs.vocab:samp_floor_enum](https://w3id.org/mixs/vocab/samp_floor_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampMdEnum.md b/mixs6/SampMdEnum.md new file mode 100644 index 00000000..19366ebf --- /dev/null +++ b/mixs6/SampMdEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_md_enum + + + + +URI: [mixs.vocab:samp_md_enum](https://w3id.org/mixs/vocab/samp_md_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampSubtypeEnum.md b/mixs6/SampSubtypeEnum.md new file mode 100644 index 00000000..59bd72fa --- /dev/null +++ b/mixs6/SampSubtypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_subtype_enum + + + + +URI: [mixs.vocab:samp_subtype_enum](https://w3id.org/mixs/vocab/samp_subtype_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampTypeEnum.md b/mixs6/SampTypeEnum.md new file mode 100644 index 00000000..9a475694 --- /dev/null +++ b/mixs6/SampTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_type_enum + + + + +URI: [mixs.vocab:samp_type_enum](https://w3id.org/mixs/vocab/samp_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampWeatherEnum.md b/mixs6/SampWeatherEnum.md new file mode 100644 index 00000000..eb0dc515 --- /dev/null +++ b/mixs6/SampWeatherEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_weather_enum + + + + +URI: [mixs.vocab:samp_weather_enum](https://w3id.org/mixs/vocab/samp_weather_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SeasonUseEnum.md b/mixs6/SeasonUseEnum.md new file mode 100644 index 00000000..db48c17e --- /dev/null +++ b/mixs6/SeasonUseEnum.md @@ -0,0 +1,19 @@ + +# Enum: season_use_enum + + + + +URI: [mixs.vocab:season_use_enum](https://w3id.org/mixs/vocab/season_use_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Sediment.md b/mixs6/Sediment.md new file mode 100644 index 00000000..1f1461b7 --- /dev/null +++ b/mixs6/Sediment.md @@ -0,0 +1,333 @@ + +# Class: Sediment + + +sediment + +URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIUVIG],[SedimentMISAG],[SedimentMIMARKSSurvey],[SedimentMIMARKSSpecimen],[SedimentMIMAG],[SedimentMIGSVirus],[SedimentMIGSPlant],[SedimentMIGSOrg],[SedimentMIGSEukaryote],[SedimentMIGSBacteria],[SedimentME],[QuantityValue]OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None diff --git a/mixs6/SedimentMIGSBacteria.md b/mixs6/SedimentMIGSBacteria.md new file mode 100644 index 00000000..ffc2078d --- /dev/null +++ b/mixs6/SedimentMIGSBacteria.md @@ -0,0 +1,564 @@ + +# Class: SedimentMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSBacteria](https://w3id.org/mixs/vocab/SedimentMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSBacteria],[Sediment]^-[SedimentMIGSBacteria],[Sediment],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIGSEukaryote.md b/mixs6/SedimentMIGSEukaryote.md new file mode 100644 index 00000000..8c4115f2 --- /dev/null +++ b/mixs6/SedimentMIGSEukaryote.md @@ -0,0 +1,564 @@ + +# Class: SedimentMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSEukaryote](https://w3id.org/mixs/vocab/SedimentMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Sediment]^-[SedimentMIGSEukaryote],[Sediment],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIGSPlant.md b/mixs6/SedimentMIGSPlant.md new file mode 100644 index 00000000..6798ae18 --- /dev/null +++ b/mixs6/SedimentMIGSPlant.md @@ -0,0 +1,534 @@ + +# Class: SedimentMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSPlant](https://w3id.org/mixs/vocab/SedimentMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Sediment]^-[SedimentMIGSPlant],[Sediment],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIGSVirus.md b/mixs6/SedimentMIGSVirus.md new file mode 100644 index 00000000..bbeeb795 --- /dev/null +++ b/mixs6/SedimentMIGSVirus.md @@ -0,0 +1,559 @@ + +# Class: SedimentMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSVirus](https://w3id.org/mixs/vocab/SedimentMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Sediment]^-[SedimentMIGSVirus],[Sediment],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/SedimentMIMARKSSpecimen.md b/mixs6/SedimentMIMARKSSpecimen.md new file mode 100644 index 00000000..0567f241 --- /dev/null +++ b/mixs6/SedimentMIMARKSSpecimen.md @@ -0,0 +1,484 @@ + +# Class: SedimentMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment + +URI: [mixs.vocab:SedimentMIMARKSSpecimen](https://w3id.org/mixs/vocab/SedimentMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Sediment]^-[SedimentMIMARKSSpecimen],[Sediment],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIMARKSSurvey.md b/mixs6/SedimentMIMARKSSurvey.md new file mode 100644 index 00000000..6175819c --- /dev/null +++ b/mixs6/SedimentMIMARKSSurvey.md @@ -0,0 +1,464 @@ + +# Class: SedimentMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package sediment + +URI: [mixs.vocab:SedimentMIMARKSSurvey](https://w3id.org/mixs/vocab/SedimentMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Sediment]^-[SedimentMIMARKSSurvey],[Sediment],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMe.md b/mixs6/SedimentMe.md new file mode 100644 index 00000000..6079b26a --- /dev/null +++ b/mixs6/SedimentMe.md @@ -0,0 +1,499 @@ + +# Class: SedimentME + + +Combinatorial checklist Metagenome or Environmental with environmental package sediment + +URI: [mixs.vocab:SedimentME](https://w3id.org/mixs/vocab/SedimentME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Sediment]^-[SedimentME],[Sediment],[QuantityValue],[ME]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsOrg.md b/mixs6/SedimentMigsOrg.md new file mode 100644 index 00000000..983e6a4d --- /dev/null +++ b/mixs6/SedimentMigsOrg.md @@ -0,0 +1,519 @@ + +# Class: SedimentMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSOrg](https://w3id.org/mixs/vocab/SedimentMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Sediment]^-[SedimentMIGSOrg],[Sediment],[QuantityValue],[MIGSOrg]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMimag.md b/mixs6/SedimentMimag.md new file mode 100644 index 00000000..458a33ae --- /dev/null +++ b/mixs6/SedimentMimag.md @@ -0,0 +1,574 @@ + +# Class: SedimentMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package sediment + +URI: [mixs.vocab:SedimentMIMAG](https://w3id.org/mixs/vocab/SedimentMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Sediment]^-[SedimentMIMAG],[Sediment],[QuantityValue],[MIMAG]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMisag.md b/mixs6/SedimentMisag.md new file mode 100644 index 00000000..e6f79eb2 --- /dev/null +++ b/mixs6/SedimentMisag.md @@ -0,0 +1,579 @@ + +# Class: SedimentMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package sediment + +URI: [mixs.vocab:SedimentMISAG](https://w3id.org/mixs/vocab/SedimentMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Sediment]^-[SedimentMISAG],[Sediment],[QuantityValue],[MISAG]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMiuvig.md b/mixs6/SedimentMiuvig.md new file mode 100644 index 00000000..3cb6ddab --- /dev/null +++ b/mixs6/SedimentMiuvig.md @@ -0,0 +1,649 @@ + +# Class: SedimentMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package sediment + +URI: [mixs.vocab:SedimentMIUVIG](https://w3id.org/mixs/vocab/SedimentMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Sediment]^-[SedimentMIUVIG],[Sediment],[QuantityValue],[MIUVIG]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentTypeEnum.md b/mixs6/SedimentTypeEnum.md new file mode 100644 index 00000000..02433ebd --- /dev/null +++ b/mixs6/SedimentTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: sediment_type_enum + + + + +URI: [mixs.vocab:sediment_type_enum](https://w3id.org/mixs/vocab/sediment_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SeqMethEnum.md b/mixs6/SeqMethEnum.md new file mode 100644 index 00000000..c21edb54 --- /dev/null +++ b/mixs6/SeqMethEnum.md @@ -0,0 +1,19 @@ + +# Enum: seq_meth_enum + + + + +URI: [mixs.vocab:seq_meth_enum](https://w3id.org/mixs/vocab/seq_meth_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ShadingDeviceCondEnum.md b/mixs6/ShadingDeviceCondEnum.md new file mode 100644 index 00000000..6f9708f3 --- /dev/null +++ b/mixs6/ShadingDeviceCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: shading_device_cond_enum + + + + +URI: [mixs.vocab:shading_device_cond_enum](https://w3id.org/mixs/vocab/shading_device_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ShadingDeviceTypeEnum.md b/mixs6/ShadingDeviceTypeEnum.md new file mode 100644 index 00000000..5a805ada --- /dev/null +++ b/mixs6/ShadingDeviceTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: shading_device_type_enum + + + + +URI: [mixs.vocab:shading_device_type_enum](https://w3id.org/mixs/vocab/shading_device_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SingleCellLysisApprEnum.md b/mixs6/SingleCellLysisApprEnum.md new file mode 100644 index 00000000..b76f64f4 --- /dev/null +++ b/mixs6/SingleCellLysisApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: single_cell_lysis_appr_enum + + + + +URI: [mixs.vocab:single_cell_lysis_appr_enum](https://w3id.org/mixs/vocab/single_cell_lysis_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Soil.md b/mixs6/Soil.md new file mode 100644 index 00000000..bd35c6f5 --- /dev/null +++ b/mixs6/Soil.md @@ -0,0 +1,277 @@ + +# Class: Soil + + +soil + +URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIUVIG],[SoilMISAG],[SoilMIMARKSSurvey],[SoilMIMARKSSpecimen],[SoilMIMAG],[SoilMIGSVirus],[SoilMIGSPlant],[SoilMIGSOrg],[SoilMIGSEukaryote],[SoilMIGSBacteria],[SoilME],[QuantityValue]OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMIGSBacteria.md b/mixs6/SoilMIGSBacteria.md new file mode 100644 index 00000000..2a262e74 --- /dev/null +++ b/mixs6/SoilMIGSBacteria.md @@ -0,0 +1,508 @@ + +# Class: SoilMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + +URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Soil]^-[SoilMIGSBacteria],[Soil],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIGSEukaryote.md b/mixs6/SoilMIGSEukaryote.md new file mode 100644 index 00000000..ba9736cf --- /dev/null +++ b/mixs6/SoilMIGSEukaryote.md @@ -0,0 +1,508 @@ + +# Class: SoilMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package soil + +URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Soil]^-[SoilMIGSEukaryote],[Soil],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIGSPlant.md b/mixs6/SoilMIGSPlant.md new file mode 100644 index 00000000..1da40d48 --- /dev/null +++ b/mixs6/SoilMIGSPlant.md @@ -0,0 +1,478 @@ + +# Class: SoilMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package soil + +URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Soil]^-[SoilMIGSPlant],[Soil],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIGSVirus.md b/mixs6/SoilMIGSVirus.md new file mode 100644 index 00000000..75bb3b12 --- /dev/null +++ b/mixs6/SoilMIGSVirus.md @@ -0,0 +1,503 @@ + +# Class: SoilMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + +URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Soil]^-[SoilMIGSVirus],[Soil],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/SoilMIMARKSSpecimen.md b/mixs6/SoilMIMARKSSpecimen.md new file mode 100644 index 00000000..18d7b82a --- /dev/null +++ b/mixs6/SoilMIMARKSSpecimen.md @@ -0,0 +1,428 @@ + +# Class: SoilMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package soil + +URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Soil]^-[SoilMIMARKSSpecimen],[Soil],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIMARKSSurvey.md b/mixs6/SoilMIMARKSSurvey.md new file mode 100644 index 00000000..7da6c55e --- /dev/null +++ b/mixs6/SoilMIMARKSSurvey.md @@ -0,0 +1,408 @@ + +# Class: SoilMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil + +URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Soil]^-[SoilMIMARKSSurvey],[Soil],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMe.md b/mixs6/SoilMe.md new file mode 100644 index 00000000..b2568dd7 --- /dev/null +++ b/mixs6/SoilMe.md @@ -0,0 +1,443 @@ + +# Class: SoilME + + +Combinatorial checklist Metagenome or Environmental with environmental package soil + +URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Soil]^-[SoilME],[Soil],[QuantityValue],[ME]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMigsOrg.md b/mixs6/SoilMigsOrg.md new file mode 100644 index 00000000..a393f06c --- /dev/null +++ b/mixs6/SoilMigsOrg.md @@ -0,0 +1,463 @@ + +# Class: SoilMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package soil + +URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Soil]^-[SoilMIGSOrg],[Soil],[QuantityValue],[MIGSOrg]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMimag.md b/mixs6/SoilMimag.md new file mode 100644 index 00000000..9d27e573 --- /dev/null +++ b/mixs6/SoilMimag.md @@ -0,0 +1,518 @@ + +# Class: SoilMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil + +URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Soil]^-[SoilMIMAG],[Soil],[QuantityValue],[MIMAG]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMisag.md b/mixs6/SoilMisag.md new file mode 100644 index 00000000..489e5e81 --- /dev/null +++ b/mixs6/SoilMisag.md @@ -0,0 +1,523 @@ + +# Class: SoilMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package soil + +URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Soil]^-[SoilMISAG],[Soil],[QuantityValue],[MISAG]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMiuvig.md b/mixs6/SoilMiuvig.md new file mode 100644 index 00000000..76fa154d --- /dev/null +++ b/mixs6/SoilMiuvig.md @@ -0,0 +1,593 @@ + +# Class: SoilMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package soil + +URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Soil]^-[SoilMIUVIG],[Soil],[QuantityValue],[MIUVIG]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [Date](types/Date.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [Date](types/Date.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [Date](types/Date.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SortTechEnum.md b/mixs6/SortTechEnum.md new file mode 100644 index 00000000..e2c68a73 --- /dev/null +++ b/mixs6/SortTechEnum.md @@ -0,0 +1,19 @@ + +# Enum: sort_tech_enum + + + + +URI: [mixs.vocab:sort_tech_enum](https://w3id.org/mixs/vocab/sort_tech_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SourceUvigEnum.md b/mixs6/SourceUvigEnum.md new file mode 100644 index 00000000..ded313b3 --- /dev/null +++ b/mixs6/SourceUvigEnum.md @@ -0,0 +1,19 @@ + +# Enum: source_uvig_enum + + + + +URI: [mixs.vocab:source_uvig_enum](https://w3id.org/mixs/vocab/source_uvig_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SpecialDietEnum.md b/mixs6/SpecialDietEnum.md new file mode 100644 index 00000000..9dba3a66 --- /dev/null +++ b/mixs6/SpecialDietEnum.md @@ -0,0 +1,19 @@ + +# Enum: special_diet_enum + + + + +URI: [mixs.vocab:special_diet_enum](https://w3id.org/mixs/vocab/special_diet_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SpecificEnum.md b/mixs6/SpecificEnum.md new file mode 100644 index 00000000..00553595 --- /dev/null +++ b/mixs6/SpecificEnum.md @@ -0,0 +1,19 @@ + +# Enum: specific_enum + + + + +URI: [mixs.vocab:specific_enum](https://w3id.org/mixs/vocab/specific_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrDepEnvEnum.md b/mixs6/SrDepEnvEnum.md new file mode 100644 index 00000000..49ea3e6e --- /dev/null +++ b/mixs6/SrDepEnvEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_dep_env_enum + + + + +URI: [mixs.vocab:sr_dep_env_enum](https://w3id.org/mixs/vocab/sr_dep_env_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrGeolAgeEnum.md b/mixs6/SrGeolAgeEnum.md new file mode 100644 index 00000000..db971dee --- /dev/null +++ b/mixs6/SrGeolAgeEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_geol_age_enum + + + + +URI: [mixs.vocab:sr_geol_age_enum](https://w3id.org/mixs/vocab/sr_geol_age_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrKerogTypeEnum.md b/mixs6/SrKerogTypeEnum.md new file mode 100644 index 00000000..4b537dc6 --- /dev/null +++ b/mixs6/SrKerogTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_kerog_type_enum + + + + +URI: [mixs.vocab:sr_kerog_type_enum](https://w3id.org/mixs/vocab/sr_kerog_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrLithologyEnum.md b/mixs6/SrLithologyEnum.md new file mode 100644 index 00000000..74791f8c --- /dev/null +++ b/mixs6/SrLithologyEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_lithology_enum + + + + +URI: [mixs.vocab:sr_lithology_enum](https://w3id.org/mixs/vocab/sr_lithology_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/StudyCompltStatEnum.md b/mixs6/StudyCompltStatEnum.md new file mode 100644 index 00000000..8c25de2c --- /dev/null +++ b/mixs6/StudyCompltStatEnum.md @@ -0,0 +1,19 @@ + +# Enum: study_complt_stat_enum + + + + +URI: [mixs.vocab:study_complt_stat_enum](https://w3id.org/mixs/vocab/study_complt_stat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SubstructureTypeEnum.md b/mixs6/SubstructureTypeEnum.md new file mode 100644 index 00000000..be4a1a03 --- /dev/null +++ b/mixs6/SubstructureTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: substructure_type_enum + + + + +URI: [mixs.vocab:substructure_type_enum](https://w3id.org/mixs/vocab/substructure_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SurfAirContEnum.md b/mixs6/SurfAirContEnum.md new file mode 100644 index 00000000..d305ad79 --- /dev/null +++ b/mixs6/SurfAirContEnum.md @@ -0,0 +1,19 @@ + +# Enum: surf_air_cont_enum + + + + +URI: [mixs.vocab:surf_air_cont_enum](https://w3id.org/mixs/vocab/surf_air_cont_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SurfMaterialEnum.md b/mixs6/SurfMaterialEnum.md new file mode 100644 index 00000000..08d405cd --- /dev/null +++ b/mixs6/SurfMaterialEnum.md @@ -0,0 +1,19 @@ + +# Enum: surf_material_enum + + + + +URI: [mixs.vocab:surf_material_enum](https://w3id.org/mixs/vocab/surf_material_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TaxIdentEnum.md b/mixs6/TaxIdentEnum.md new file mode 100644 index 00000000..199885e6 --- /dev/null +++ b/mixs6/TaxIdentEnum.md @@ -0,0 +1,19 @@ + +# Enum: tax_ident_enum + + + + +URI: [mixs.vocab:tax_ident_enum](https://w3id.org/mixs/vocab/tax_ident_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TidalStageEnum.md b/mixs6/TidalStageEnum.md new file mode 100644 index 00000000..1e58cb2f --- /dev/null +++ b/mixs6/TidalStageEnum.md @@ -0,0 +1,19 @@ + +# Enum: tidal_stage_enum + + + + +URI: [mixs.vocab:tidal_stage_enum](https://w3id.org/mixs/vocab/tidal_stage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TillageEnum.md b/mixs6/TillageEnum.md new file mode 100644 index 00000000..0779cd90 --- /dev/null +++ b/mixs6/TillageEnum.md @@ -0,0 +1,19 @@ + +# Enum: tillage_enum + + + + +URI: [mixs.vocab:tillage_enum](https://w3id.org/mixs/vocab/tillage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrainLineEnum.md b/mixs6/TrainLineEnum.md new file mode 100644 index 00000000..3a7801bd --- /dev/null +++ b/mixs6/TrainLineEnum.md @@ -0,0 +1,19 @@ + +# Enum: train_line_enum + + + + +URI: [mixs.vocab:train_line_enum](https://w3id.org/mixs/vocab/train_line_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrainStatLocEnum.md b/mixs6/TrainStatLocEnum.md new file mode 100644 index 00000000..96b361ce --- /dev/null +++ b/mixs6/TrainStatLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: train_stat_loc_enum + + + + +URI: [mixs.vocab:train_stat_loc_enum](https://w3id.org/mixs/vocab/train_stat_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrainStopLocEnum.md b/mixs6/TrainStopLocEnum.md new file mode 100644 index 00000000..bffbb402 --- /dev/null +++ b/mixs6/TrainStopLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: train_stop_loc_enum + + + + +URI: [mixs.vocab:train_stop_loc_enum](https://w3id.org/mixs/vocab/train_stop_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrophicLevelEnum.md b/mixs6/TrophicLevelEnum.md new file mode 100644 index 00000000..a433f913 --- /dev/null +++ b/mixs6/TrophicLevelEnum.md @@ -0,0 +1,19 @@ + +# Enum: trophic_level_enum + + + + +URI: [mixs.vocab:trophic_level_enum](https://w3id.org/mixs/vocab/trophic_level_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/VirusEnrichApprEnum.md b/mixs6/VirusEnrichApprEnum.md new file mode 100644 index 00000000..0be83d9a --- /dev/null +++ b/mixs6/VirusEnrichApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: virus_enrich_appr_enum + + + + +URI: [mixs.vocab:virus_enrich_appr_enum](https://w3id.org/mixs/vocab/virus_enrich_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/VisMediaEnum.md b/mixs6/VisMediaEnum.md new file mode 100644 index 00000000..736292bb --- /dev/null +++ b/mixs6/VisMediaEnum.md @@ -0,0 +1,19 @@ + +# Enum: vis_media_enum + + + + +URI: [mixs.vocab:vis_media_enum](https://w3id.org/mixs/vocab/vis_media_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallConstTypeEnum.md b/mixs6/WallConstTypeEnum.md new file mode 100644 index 00000000..526c7222 --- /dev/null +++ b/mixs6/WallConstTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_const_type_enum + + + + +URI: [mixs.vocab:wall_const_type_enum](https://w3id.org/mixs/vocab/wall_const_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallFinishMatEnum.md b/mixs6/WallFinishMatEnum.md new file mode 100644 index 00000000..02bfe0bb --- /dev/null +++ b/mixs6/WallFinishMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_finish_mat_enum + + + + +URI: [mixs.vocab:wall_finish_mat_enum](https://w3id.org/mixs/vocab/wall_finish_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallLocEnum.md b/mixs6/WallLocEnum.md new file mode 100644 index 00000000..cd3fa234 --- /dev/null +++ b/mixs6/WallLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_loc_enum + + + + +URI: [mixs.vocab:wall_loc_enum](https://w3id.org/mixs/vocab/wall_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallSurfTreatmentEnum.md b/mixs6/WallSurfTreatmentEnum.md new file mode 100644 index 00000000..a33e5e15 --- /dev/null +++ b/mixs6/WallSurfTreatmentEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_surf_treatment_enum + + + + +URI: [mixs.vocab:wall_surf_treatment_enum](https://w3id.org/mixs/vocab/wall_surf_treatment_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallTextureEnum.md b/mixs6/WallTextureEnum.md new file mode 100644 index 00000000..2f970b73 --- /dev/null +++ b/mixs6/WallTextureEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_texture_enum + + + + +URI: [mixs.vocab:wall_texture_enum](https://w3id.org/mixs/vocab/wall_texture_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WastewaterSludge.md b/mixs6/WastewaterSludge.md new file mode 100644 index 00000000..3e6e6e08 --- /dev/null +++ b/mixs6/WastewaterSludge.md @@ -0,0 +1,217 @@ + +# Class: WastewaterSludge + + +wastewater/sludge + +URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIUVIG],[WastewaterSludgeMISAG],[WastewaterSludgeMIMARKSSurvey],[WastewaterSludgeMIMARKSSpecimen],[WastewaterSludgeMIMAG],[WastewaterSludgeMIGSVirus],[WastewaterSludgeMIGSPlant],[WastewaterSludgeMIGSOrg],[WastewaterSludgeMIGSEukaryote],[WastewaterSludgeMIGSBacteria],[WastewaterSludgeME],[QuantityValue]OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMIGSBacteria.md b/mixs6/WastewaterSludgeMIGSBacteria.md new file mode 100644 index 00000000..0ebf375e --- /dev/null +++ b/mixs6/WastewaterSludgeMIGSBacteria.md @@ -0,0 +1,448 @@ + +# Class: WastewaterSludgeMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSBacteria](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSBacteria],[WastewaterSludge]^-[WastewaterSludgeMIGSBacteria],[WastewaterSludge],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIGSEukaryote.md b/mixs6/WastewaterSludgeMIGSEukaryote.md new file mode 100644 index 00000000..95ef1235 --- /dev/null +++ b/mixs6/WastewaterSludgeMIGSEukaryote.md @@ -0,0 +1,448 @@ + +# Class: WastewaterSludgeMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSEukaryote](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSEukaryote],[WastewaterSludge]^-[WastewaterSludgeMIGSEukaryote],[WastewaterSludge],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIGSPlant.md b/mixs6/WastewaterSludgeMIGSPlant.md new file mode 100644 index 00000000..35088ae6 --- /dev/null +++ b/mixs6/WastewaterSludgeMIGSPlant.md @@ -0,0 +1,418 @@ + +# Class: WastewaterSludgeMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSPlant](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSPlant],[WastewaterSludge]^-[WastewaterSludgeMIGSPlant],[WastewaterSludge],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIGSVirus.md b/mixs6/WastewaterSludgeMIGSVirus.md new file mode 100644 index 00000000..79c26233 --- /dev/null +++ b/mixs6/WastewaterSludgeMIGSVirus.md @@ -0,0 +1,443 @@ + +# Class: WastewaterSludgeMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSVirus](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSVirus],[WastewaterSludge]^-[WastewaterSludgeMIGSVirus],[WastewaterSludge],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/WastewaterSludgeMIMARKSSpecimen.md b/mixs6/WastewaterSludgeMIMARKSSpecimen.md new file mode 100644 index 00000000..ca926300 --- /dev/null +++ b/mixs6/WastewaterSludgeMIMARKSSpecimen.md @@ -0,0 +1,368 @@ + +# Class: WastewaterSludgeMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIMARKSSpecimen](https://w3id.org/mixs/vocab/WastewaterSludgeMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSpecimen],[WastewaterSludge],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIMARKSSurvey.md b/mixs6/WastewaterSludgeMIMARKSSurvey.md new file mode 100644 index 00000000..95c96308 --- /dev/null +++ b/mixs6/WastewaterSludgeMIMARKSSurvey.md @@ -0,0 +1,348 @@ + +# Class: WastewaterSludgeMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIMARKSSurvey](https://w3id.org/mixs/vocab/WastewaterSludgeMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSurvey],[WastewaterSludge],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMe.md b/mixs6/WastewaterSludgeMe.md new file mode 100644 index 00000000..60f42f51 --- /dev/null +++ b/mixs6/WastewaterSludgeMe.md @@ -0,0 +1,383 @@ + +# Class: WastewaterSludgeME + + +Combinatorial checklist Metagenome or Environmental with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeME](https://w3id.org/mixs/vocab/WastewaterSludgeME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[ME],[WastewaterSludge]^-[WastewaterSludgeME],[WastewaterSludge],[QuantityValue],[ME]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsOrg.md b/mixs6/WastewaterSludgeMigsOrg.md new file mode 100644 index 00000000..0c9d239f --- /dev/null +++ b/mixs6/WastewaterSludgeMigsOrg.md @@ -0,0 +1,403 @@ + +# Class: WastewaterSludgeMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSOrg](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSOrg],[WastewaterSludge]^-[WastewaterSludgeMIGSOrg],[WastewaterSludge],[QuantityValue],[MIGSOrg]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMimag.md b/mixs6/WastewaterSludgeMimag.md new file mode 100644 index 00000000..9d636a17 --- /dev/null +++ b/mixs6/WastewaterSludgeMimag.md @@ -0,0 +1,458 @@ + +# Class: WastewaterSludgeMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIMAG](https://w3id.org/mixs/vocab/WastewaterSludgeMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMAG],[WastewaterSludge]^-[WastewaterSludgeMIMAG],[WastewaterSludge],[QuantityValue],[MIMAG]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMisag.md b/mixs6/WastewaterSludgeMisag.md new file mode 100644 index 00000000..6ca39949 --- /dev/null +++ b/mixs6/WastewaterSludgeMisag.md @@ -0,0 +1,463 @@ + +# Class: WastewaterSludgeMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMISAG](https://w3id.org/mixs/vocab/WastewaterSludgeMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MISAG],[WastewaterSludge]^-[WastewaterSludgeMISAG],[WastewaterSludge],[QuantityValue],[MISAG]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMiuvig.md b/mixs6/WastewaterSludgeMiuvig.md new file mode 100644 index 00000000..0d955ed0 --- /dev/null +++ b/mixs6/WastewaterSludgeMiuvig.md @@ -0,0 +1,533 @@ + +# Class: WastewaterSludgeMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIUVIG](https://w3id.org/mixs/vocab/WastewaterSludgeMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIUVIG],[WastewaterSludge]^-[WastewaterSludgeMIUVIG],[WastewaterSludge],[QuantityValue],[MIUVIG]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Water.md b/mixs6/Water.md new file mode 100644 index 00000000..28c7f802 --- /dev/null +++ b/mixs6/Water.md @@ -0,0 +1,393 @@ + +# Class: Water + + +water + +URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIUVIG],[WaterMISAG],[WaterMIMARKSSurvey],[WaterMIMARKSSpecimen],[WaterMIMAG],[WaterMIGSVirus],[WaterMIGSPlant],[WaterMIGSOrg],[WaterMIGSEukaryote],[WaterMIGSBacteria],[WaterME],[QuantityValue]OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterFeatTypeEnum.md b/mixs6/WaterFeatTypeEnum.md new file mode 100644 index 00000000..6de4e273 --- /dev/null +++ b/mixs6/WaterFeatTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: water_feat_type_enum + + + + +URI: [mixs.vocab:water_feat_type_enum](https://w3id.org/mixs/vocab/water_feat_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WaterMIGSBacteria.md b/mixs6/WaterMIGSBacteria.md new file mode 100644 index 00000000..271f653a --- /dev/null +++ b/mixs6/WaterMIGSBacteria.md @@ -0,0 +1,624 @@ + +# Class: WaterMIGSBacteria + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + +URI: [mixs.vocab:WaterMIGSBacteria](https://w3id.org/mixs/vocab/WaterMIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSBacteria],[Water]^-[WaterMIGSBacteria],[Water],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIGSEukaryote.md b/mixs6/WaterMIGSEukaryote.md new file mode 100644 index 00000000..52868af6 --- /dev/null +++ b/mixs6/WaterMIGSEukaryote.md @@ -0,0 +1,624 @@ + +# Class: WaterMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package water + +URI: [mixs.vocab:WaterMIGSEukaryote](https://w3id.org/mixs/vocab/WaterMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Water]^-[WaterMIGSEukaryote],[Water],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIGSPlant.md b/mixs6/WaterMIGSPlant.md new file mode 100644 index 00000000..54858469 --- /dev/null +++ b/mixs6/WaterMIGSPlant.md @@ -0,0 +1,594 @@ + +# Class: WaterMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package water + +URI: [mixs.vocab:WaterMIGSPlant](https://w3id.org/mixs/vocab/WaterMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Water]^-[WaterMIGSPlant],[Water],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIGSVirus.md b/mixs6/WaterMIGSVirus.md new file mode 100644 index 00000000..1439c0ab --- /dev/null +++ b/mixs6/WaterMIGSVirus.md @@ -0,0 +1,619 @@ + +# Class: WaterMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + +URI: [mixs.vocab:WaterMIGSVirus](https://w3id.org/mixs/vocab/WaterMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Water]^-[WaterMIGSVirus],[Water],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/WaterMIMARKSSpecimen.md b/mixs6/WaterMIMARKSSpecimen.md new file mode 100644 index 00000000..9299fcc4 --- /dev/null +++ b/mixs6/WaterMIMARKSSpecimen.md @@ -0,0 +1,544 @@ + +# Class: WaterMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package water + +URI: [mixs.vocab:WaterMIMARKSSpecimen](https://w3id.org/mixs/vocab/WaterMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Water]^-[WaterMIMARKSSpecimen],[Water],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIMARKSSurvey.md b/mixs6/WaterMIMARKSSurvey.md new file mode 100644 index 00000000..c4e515e3 --- /dev/null +++ b/mixs6/WaterMIMARKSSurvey.md @@ -0,0 +1,524 @@ + +# Class: WaterMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package water + +URI: [mixs.vocab:WaterMIMARKSSurvey](https://w3id.org/mixs/vocab/WaterMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Water]^-[WaterMIMARKSSurvey],[Water],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMe.md b/mixs6/WaterMe.md new file mode 100644 index 00000000..5dc05831 --- /dev/null +++ b/mixs6/WaterMe.md @@ -0,0 +1,559 @@ + +# Class: WaterME + + +Combinatorial checklist Metagenome or Environmental with environmental package water + +URI: [mixs.vocab:WaterME](https://w3id.org/mixs/vocab/WaterME) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Water]^-[WaterME],[Water],[QuantityValue],[ME]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [ME](ME.md) - Metagenome or Environmental + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from ME: + + * [ME➞adapters](ME_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞annot](ME_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_name](ME_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞assembly_qual](ME_assembly_qual.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞assembly_software](ME_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞env_package](ME_env_package.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞experimental_factor](ME_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞feat_pred](ME_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞investigation_type](ME_investigation_type.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞lib_layout](ME_lib_layout.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_screen](ME_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_size](ME_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞lib_vector](ME_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞mid](ME_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞number_contig](ME_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞project_name](ME_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞ref_db](ME_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT + * range: + +### Mixed in from ME: + + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sample_name](ME_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞seq_meth](ME_seq_meth.md) REQ + * range: + +### Mixed in from ME: + + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞size_frac](ME_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞sop](ME_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞source_mat_id](ME_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞tax_class](ME_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from ME: + + * [ME➞url](ME_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMigsOrg.md b/mixs6/WaterMigsOrg.md new file mode 100644 index 00000000..73f6a989 --- /dev/null +++ b/mixs6/WaterMigsOrg.md @@ -0,0 +1,579 @@ + +# Class: WaterMIGSOrg + + +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package water + +URI: [mixs.vocab:WaterMIGSOrg](https://w3id.org/mixs/vocab/WaterMIGSOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Water]^-[WaterMIGSOrg],[Water],[QuantityValue],[MIGSOrg]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS org: + + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞annot](MIGS_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sop](MIGS_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS org: + + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT + * range: + +### Mixed in from MIGS org: + + * [MIGS org➞url](MIGS_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMimag.md b/mixs6/WaterMimag.md new file mode 100644 index 00000000..69803349 --- /dev/null +++ b/mixs6/WaterMimag.md @@ -0,0 +1,634 @@ + +# Class: WaterMIMAG + + +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package water + +URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Water]^-[WaterMIMAG],[Water],[QuantityValue],[MIMAG]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMAG: + + * [MIMAG➞adapters](MIMAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞annot](MIMAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞env_package](MIMAG_env_package.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞mid](MIMAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞project_name](MIMAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sop](MIMAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ + * range: + +### Mixed in from MIMAG: + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞trnas](MIMAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞url](MIMAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMAG: + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMisag.md b/mixs6/WaterMisag.md new file mode 100644 index 00000000..169665f2 --- /dev/null +++ b/mixs6/WaterMisag.md @@ -0,0 +1,639 @@ + +# Class: WaterMISAG + + +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package water + +URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Water]^-[WaterMISAG],[Water],[QuantityValue],[MISAG]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MISAG: + + * [MISAG➞adapters](MISAG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞annot](MISAG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_score](MISAG_compl_score.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞compl_software](MISAG_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_score](MISAG_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞env_package](MISAG_env_package.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_size](MISAG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞mid](MISAG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞number_contig](MISAG_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞project_name](MISAG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞ref_db](MISAG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MISAG: + + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_name](MISAG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞size_frac](MISAG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sop](MISAG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_class](MISAG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ + * range: + +### Mixed in from MISAG: + + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞trnas](MISAG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞url](MISAG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from MISAG: + + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMiuvig.md b/mixs6/WaterMiuvig.md new file mode 100644 index 00000000..cbe1713c --- /dev/null +++ b/mixs6/WaterMiuvig.md @@ -0,0 +1,709 @@ + +# Class: WaterMIUVIG + + +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package water + +URI: [mixs.vocab:WaterMIUVIG](https://w3id.org/mixs/vocab/WaterMIUVIG) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Water]^-[WaterMIUVIG],[Water],[QuantityValue],[MIUVIG]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [Date](types/Date.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIUVIG: + + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞annot](MIUVIG_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞mid](MIUVIG_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sop](MIUVIG_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞url](MIUVIG_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ + * range: + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WeekdayEnum.md b/mixs6/WeekdayEnum.md new file mode 100644 index 00000000..4607b41b --- /dev/null +++ b/mixs6/WeekdayEnum.md @@ -0,0 +1,19 @@ + +# Enum: weekday_enum + + + + +URI: [mixs.vocab:weekday_enum](https://w3id.org/mixs/vocab/weekday_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowCondEnum.md b/mixs6/WindowCondEnum.md new file mode 100644 index 00000000..0e047652 --- /dev/null +++ b/mixs6/WindowCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_cond_enum + + + + +URI: [mixs.vocab:window_cond_enum](https://w3id.org/mixs/vocab/window_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowCoverEnum.md b/mixs6/WindowCoverEnum.md new file mode 100644 index 00000000..5a1d6074 --- /dev/null +++ b/mixs6/WindowCoverEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_cover_enum + + + + +URI: [mixs.vocab:window_cover_enum](https://w3id.org/mixs/vocab/window_cover_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowHorizPosEnum.md b/mixs6/WindowHorizPosEnum.md new file mode 100644 index 00000000..2f1701ed --- /dev/null +++ b/mixs6/WindowHorizPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_horiz_pos_enum + + + + +URI: [mixs.vocab:window_horiz_pos_enum](https://w3id.org/mixs/vocab/window_horiz_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowLocEnum.md b/mixs6/WindowLocEnum.md new file mode 100644 index 00000000..1a976f3a --- /dev/null +++ b/mixs6/WindowLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_loc_enum + + + + +URI: [mixs.vocab:window_loc_enum](https://w3id.org/mixs/vocab/window_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowMatEnum.md b/mixs6/WindowMatEnum.md new file mode 100644 index 00000000..0a65204c --- /dev/null +++ b/mixs6/WindowMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_mat_enum + + + + +URI: [mixs.vocab:window_mat_enum](https://w3id.org/mixs/vocab/window_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowTypeEnum.md b/mixs6/WindowTypeEnum.md new file mode 100644 index 00000000..333a57b8 --- /dev/null +++ b/mixs6/WindowTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_type_enum + + + + +URI: [mixs.vocab:window_type_enum](https://w3id.org/mixs/vocab/window_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowVertPosEnum.md b/mixs6/WindowVertPosEnum.md new file mode 100644 index 00000000..137b1ec9 --- /dev/null +++ b/mixs6/WindowVertPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_vert_pos_enum + + + + +URI: [mixs.vocab:window_vert_pos_enum](https://w3id.org/mixs/vocab/window_vert_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/abs_air_humidity.md b/mixs6/abs_air_humidity.md new file mode 100644 index 00000000..883bf48a --- /dev/null +++ b/mixs6/abs_air_humidity.md @@ -0,0 +1,48 @@ + +# Slot: abs_air_humidity + + +Actual mass of water vapor - mh20 - present in the air water vapor mixture + +URI: [mixs.vocab:abs_air_humidity](https://w3id.org/mixs/vocab/abs_air_humidity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | absolute air humidity | +| **Mappings:** | | MIXS:0000122 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per gram, kilogram per kilogram, kilogram, pound | +| | | Occurrence: 1 | +| | | Position: 4.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='9 gram per gram', description=None) | + diff --git a/mixs6/adapters.md b/mixs6/adapters.md new file mode 100644 index 00000000..8a40140b --- /dev/null +++ b/mixs6/adapters.md @@ -0,0 +1,43 @@ + +# Slot: adapters + + +Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + +URI: [mixs.vocab:adapters](https://w3id.org/mixs/vocab/adapters) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞adapters](ME_adapters.md) + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) + * [MIGS org➞adapters](MIGS_org_adapters.md) + * [MIGS plant➞adapters](MIGS_plant_adapters.md) + * [MIGS virus➞adapters](MIGS_virus_adapters.md) + * [MIMAG➞adapters](MIMAG_adapters.md) + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) + * [MISAG➞adapters](MISAG_adapters.md) + * [MIUVIG➞adapters](MIUVIG_adapters.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | adapters | +| **Comments:** | | Expected value: adapter A and B sequence | +| | | Position: 48.0 | +| **Examples:** | | Example(value='AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT', description=None) | + diff --git a/mixs6/add_recov_method.md b/mixs6/add_recov_method.md new file mode 100644 index 00000000..fa820018 --- /dev/null +++ b/mixs6/add_recov_method.md @@ -0,0 +1,47 @@ + +# Slot: add_recov_method + + +Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:add_recov_method](https://w3id.org/mixs/vocab/add_recov_method) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | secondary and tertiary recovery methods and start date | +| **Mappings:** | | MIXS:0001009 | +| **Comments:** | | Expected value: enumeration;timestamp | +| | | Occurrence: 1 | +| | | Position: 28.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Polymer Addition;2018-06-21T14:30Z', description=None) | + diff --git a/mixs6/additional_info.md b/mixs6/additional_info.md new file mode 100644 index 00000000..1098387f --- /dev/null +++ b/mixs6/additional_info.md @@ -0,0 +1,59 @@ + +# Slot: additional_info + + +Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + +URI: [mixs.vocab:additional_info](https://w3id.org/mixs/vocab/additional_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | additional info | +| **Mappings:** | | MIXS:0000300 | +| **Comments:** | | Expected value: text | +| | | Occurrence: 1 | +| | | Position: 94.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/address.md b/mixs6/address.md new file mode 100644 index 00000000..19d2dac4 --- /dev/null +++ b/mixs6/address.md @@ -0,0 +1,47 @@ + +# Slot: address + + +The street name and building number where the sampling occurred. + +URI: [mixs.vocab:address](https://w3id.org/mixs/vocab/address) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | address | +| **Mappings:** | | MIXS:0000218 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 27.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/adj_room.md b/mixs6/adj_room.md new file mode 100644 index 00000000..7a3dc91b --- /dev/null +++ b/mixs6/adj_room.md @@ -0,0 +1,47 @@ + +# Slot: adj_room + + +List of rooms (room number, room name) immediately adjacent to the sampling room + +URI: [mixs.vocab:adj_room](https://w3id.org/mixs/vocab/adj_room) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | adjacent rooms | +| **Mappings:** | | MIXS:0000219 | +| **Comments:** | | Expected value: room name;room number | +| | | Occurrence: 1 | +| | | Position: 28.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/aero_struc.md b/mixs6/aero_struc.md new file mode 100644 index 00000000..0c5b5f71 --- /dev/null +++ b/mixs6/aero_struc.md @@ -0,0 +1,47 @@ + +# Slot: aero_struc + + +Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + +URI: [mixs.vocab:aero_struc](https://w3id.org/mixs/vocab/aero_struc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | aerospace structure | +| **Mappings:** | | MIXS:0000773 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 29.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='plane', description=None) | + diff --git a/mixs6/agrochem_addition.md b/mixs6/agrochem_addition.md new file mode 100644 index 00000000..52e451ea --- /dev/null +++ b/mixs6/agrochem_addition.md @@ -0,0 +1,48 @@ + +# Slot: agrochem_addition + + +Addition of fertilizers, pesticides, etc. - amount and time of applications + +URI: [mixs.vocab:agrochem_addition](https://w3id.org/mixs/vocab/agrochem_addition) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/agrochemical additions | +| **Mappings:** | | MIXS:0000639 | +| **Comments:** | | Expected value: agrochemical name;agrochemical amount;timestamp | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 7.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='roundup;5 milligram per liter;2018-06-21', description=None) | + diff --git a/mixs6/air_temp.md b/mixs6/air_temp.md new file mode 100644 index 00000000..32fe90e7 --- /dev/null +++ b/mixs6/air_temp.md @@ -0,0 +1,48 @@ + +# Slot: air_temp + + +Temperature of the air at the time of sampling + +URI: [mixs.vocab:air_temp](https://w3id.org/mixs/vocab/air_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | air temperature | +| **Mappings:** | | MIXS:0000124 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 6.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='20 degree Celsius', description=None) | + diff --git a/mixs6/air_temp_regm.md b/mixs6/air_temp_regm.md new file mode 100644 index 00000000..1821389c --- /dev/null +++ b/mixs6/air_temp_regm.md @@ -0,0 +1,48 @@ + +# Slot: air_temp_regm + + +Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + +URI: [mixs.vocab:air_temp_regm](https://w3id.org/mixs/vocab/air_temp_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | air temperature regimen | +| **Mappings:** | | MIXS:0000551 | +| **Comments:** | | Expected value: temperature value;treatment interval and duration | +| | | Preferred unit: degree Celsius | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/al_sat.md b/mixs6/al_sat.md new file mode 100644 index 00000000..711f0197 --- /dev/null +++ b/mixs6/al_sat.md @@ -0,0 +1,48 @@ + +# Slot: al_sat + + +Aluminum saturation (esp. For tropical soils) + +URI: [mixs.vocab:al_sat](https://w3id.org/mixs/vocab/al_sat) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/Al saturation | +| **Mappings:** | | MIXS:0000607 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 50.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/al_sat_meth.md b/mixs6/al_sat_meth.md new file mode 100644 index 00000000..53a1459e --- /dev/null +++ b/mixs6/al_sat_meth.md @@ -0,0 +1,47 @@ + +# Slot: al_sat_meth + + +Reference or method used in determining Al saturation + +URI: [mixs.vocab:al_sat_meth](https://w3id.org/mixs/vocab/al_sat_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/Al saturation method | +| **Mappings:** | | MIXS:0000324 | +| **Comments:** | | Expected value: PMID,DOI or URL | +| | | Occurrence: 1 | +| | | Position: 51.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/alkalinity.md b/mixs6/alkalinity.md new file mode 100644 index 00000000..5f538b1a --- /dev/null +++ b/mixs6/alkalinity.md @@ -0,0 +1,120 @@ + +# Slot: alkalinity + + +Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + +URI: [mixs.vocab:alkalinity](https://w3id.org/mixs/vocab/alkalinity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | alkalinity | +| **Mappings:** | | MIXS:0000421 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milliequivalent per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 56.0 | +| | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='50 milligram per liter', description=None) | + diff --git a/mixs6/alkalinity_method.md b/mixs6/alkalinity_method.md new file mode 100644 index 00000000..5b506d6d --- /dev/null +++ b/mixs6/alkalinity_method.md @@ -0,0 +1,71 @@ + +# Slot: alkalinity_method + + +Method used for alkalinity measurement + +URI: [mixs.vocab:alkalinity_method](https://w3id.org/mixs/vocab/alkalinity_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | alkalinity method | +| **Mappings:** | | MIXS:0000298 | +| **Comments:** | | Expected value: description of method | +| | | Occurrence: 1 | +| | | Position: 57.0 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | +| **Examples:** | | Example(value='titration', description=None) | + diff --git a/mixs6/alkyl_diethers.md b/mixs6/alkyl_diethers.md new file mode 100644 index 00000000..d4ff39e8 --- /dev/null +++ b/mixs6/alkyl_diethers.md @@ -0,0 +1,72 @@ + +# Slot: alkyl_diethers + + +Concentration of alkyl diethers + +URI: [mixs.vocab:alkyl_diethers](https://w3id.org/mixs/vocab/alkyl_diethers) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | alkyl diethers | +| **Mappings:** | | MIXS:0000490 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.005 mole per liter', description=None) | + diff --git a/mixs6/alt.md b/mixs6/alt.md new file mode 100644 index 00000000..ef22d9dc --- /dev/null +++ b/mixs6/alt.md @@ -0,0 +1,237 @@ + +# Slot: alt + + +Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + +URI: [mixs.vocab:alt](https://w3id.org/mixs/vocab/alt) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | altitude | +| **Comments:** | | Expected value: measurement value | +| | | This field is used in: 3 packages: air, host-associated, miscellaneous natural or artificial environment | +| **Examples:** | | Example(value='100 meter', description=None) | + diff --git a/mixs6/aminopept_act.md b/mixs6/aminopept_act.md new file mode 100644 index 00000000..3d18d6b2 --- /dev/null +++ b/mixs6/aminopept_act.md @@ -0,0 +1,72 @@ + +# Slot: aminopept_act + + +Measurement of aminopeptidase activity + +URI: [mixs.vocab:aminopept_act](https://w3id.org/mixs/vocab/aminopept_act) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | aminopeptidase activity | +| **Mappings:** | | MIXS:0000172 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mole per liter per hour | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.269 mole per liter per hour', description=None) | + diff --git a/mixs6/ammonium.md b/mixs6/ammonium.md new file mode 100644 index 00000000..370e5033 --- /dev/null +++ b/mixs6/ammonium.md @@ -0,0 +1,108 @@ + +# Slot: ammonium + + +Concentration of ammonium in the sample + +URI: [mixs.vocab:ammonium](https://w3id.org/mixs/vocab/ammonium) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ammonium | +| **Mappings:** | | MIXS:0000427 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 63.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1.5 milligram per liter', description=None) | + diff --git a/mixs6/amniotic_fluid_color.md b/mixs6/amniotic_fluid_color.md new file mode 100644 index 00000000..dd4303fb --- /dev/null +++ b/mixs6/amniotic_fluid_color.md @@ -0,0 +1,47 @@ + +# Slot: amniotic_fluid_color + + +Specification of the color of the amniotic fluid sample + +URI: [mixs.vocab:amniotic_fluid_color](https://w3id.org/mixs/vocab/amniotic_fluid_color) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/color | +| **Mappings:** | | MIXS:0000276 | +| **Comments:** | | Expected value: color | +| | | Occurrence: 1 | +| | | Position: 39.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/amount_light.md b/mixs6/amount_light.md new file mode 100644 index 00000000..3bffc550 --- /dev/null +++ b/mixs6/amount_light.md @@ -0,0 +1,48 @@ + +# Slot: amount_light + + +The unit of illuminance and luminous emittance, measuring luminous flux per unit area + +URI: [mixs.vocab:amount_light](https://w3id.org/mixs/vocab/amount_light) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amount of light | +| **Mappings:** | | MIXS:0000140 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: lux, lumens per square meter | +| | | Occurrence: 1 | +| | | Position: 30.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ances_data.md b/mixs6/ances_data.md new file mode 100644 index 00000000..bcc38dcf --- /dev/null +++ b/mixs6/ances_data.md @@ -0,0 +1,59 @@ + +# Slot: ances_data + + +Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + +URI: [mixs.vocab:ances_data](https://w3id.org/mixs/vocab/ances_data) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ancestral data | +| **Mappings:** | | MIXS:0000247 | +| **Comments:** | | Expected value: free text | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='A/3*B', description=None) | + diff --git a/mixs6/annot.md b/mixs6/annot.md new file mode 100644 index 00000000..0c989460 --- /dev/null +++ b/mixs6/annot.md @@ -0,0 +1,42 @@ + +# Slot: annot + + +Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + +URI: [mixs.vocab:annot](https://w3id.org/mixs/vocab/annot) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞annot](ME_annot.md) + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) + * [MIGS org➞annot](MIGS_org_annot.md) + * [MIGS plant➞annot](MIGS_plant_annot.md) + * [MIGS virus➞annot](MIGS_virus_annot.md) + * [MIMAG➞annot](MIMAG_annot.md) + * [MISAG➞annot](MISAG_annot.md) + * [MIUVIG➞annot](MIUVIG_annot.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | annotation | +| **Comments:** | | Expected value: name of tool or pipeline used, or annotation source description | +| | | Position: 57.0 | +| **Examples:** | | Example(value='prokka', description=None) | + diff --git a/mixs6/annual_precpt.md b/mixs6/annual_precpt.md new file mode 100644 index 00000000..b77827ef --- /dev/null +++ b/mixs6/annual_precpt.md @@ -0,0 +1,48 @@ + +# Slot: annual_precpt + + +The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + +URI: [mixs.vocab:annual_precpt](https://w3id.org/mixs/vocab/annual_precpt) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean annual precipitation | +| **Mappings:** | | MIXS:0000644 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter | +| | | Occurrence: 1 | +| | | Position: 23.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/annual_temp.md b/mixs6/annual_temp.md new file mode 100644 index 00000000..9875d42e --- /dev/null +++ b/mixs6/annual_temp.md @@ -0,0 +1,48 @@ + +# Slot: annual_temp + + +Mean annual temperature + +URI: [mixs.vocab:annual_temp](https://w3id.org/mixs/vocab/annual_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean annual temperature | +| **Mappings:** | | MIXS:0000642 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 21.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='12.5 degree Celsius', description=None) | + diff --git a/mixs6/antibiotic_regm.md b/mixs6/antibiotic_regm.md new file mode 100644 index 00000000..8df08c68 --- /dev/null +++ b/mixs6/antibiotic_regm.md @@ -0,0 +1,48 @@ + +# Slot: antibiotic_regm + + +Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + +URI: [mixs.vocab:antibiotic_regm](https://w3id.org/mixs/vocab/antibiotic_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | antibiotic regimen | +| **Mappings:** | | MIXS:0000553 | +| **Comments:** | | Expected value: antibiotic name;antibiotic amount;treatment interval and duration | +| | | Preferred unit: milligram | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/api.md b/mixs6/api.md new file mode 100644 index 00000000..dddf3fb4 --- /dev/null +++ b/mixs6/api.md @@ -0,0 +1,60 @@ + +# Slot: api + + +API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + +URI: [mixs.vocab:api](https://w3id.org/mixs/vocab/api) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | API gravity | +| **Mappings:** | | MIXS:0000157 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degrees API | +| | | Occurrence: 1 | +| | | Position: 85.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/arch_struc.md b/mixs6/arch_struc.md new file mode 100644 index 00000000..48e8f837 --- /dev/null +++ b/mixs6/arch_struc.md @@ -0,0 +1,47 @@ + +# Slot: arch_struc + + +An architectural structure is a human-made, free-standing, immobile outdoor construction + +URI: [mixs.vocab:arch_struc](https://w3id.org/mixs/vocab/arch_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | architectural structure | +| **Mappings:** | | MIXS:0000774 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 31.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='shed', description=None) | + diff --git a/mixs6/aromatics_pc.md b/mixs6/aromatics_pc.md new file mode 100644 index 00000000..a0705e1b --- /dev/null +++ b/mixs6/aromatics_pc.md @@ -0,0 +1,60 @@ + +# Slot: aromatics_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:aromatics_pc](https://w3id.org/mixs/vocab/aromatics_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | aromatics wt% | +| **Mappings:** | | MIXS:0000133 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 90.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/asphaltenes_pc.md b/mixs6/asphaltenes_pc.md new file mode 100644 index 00000000..5b23e2ac --- /dev/null +++ b/mixs6/asphaltenes_pc.md @@ -0,0 +1,60 @@ + +# Slot: asphaltenes_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:asphaltenes_pc](https://w3id.org/mixs/vocab/asphaltenes_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | asphaltenes wt% | +| **Mappings:** | | MIXS:0000135 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 92.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/assembly_name.md b/mixs6/assembly_name.md new file mode 100644 index 00000000..7581f31e --- /dev/null +++ b/mixs6/assembly_name.md @@ -0,0 +1,42 @@ + +# Slot: assembly_name + + +Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + +URI: [mixs.vocab:assembly_name](https://w3id.org/mixs/vocab/assembly_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞assembly_name](ME_assembly_name.md) + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) + * [MISAG➞assembly_name](MISAG_assembly_name.md) + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | assembly name | +| **Comments:** | | Expected value: name and version of assembly | +| | | Position: 55.0 | +| **Examples:** | | Example(value='HuRef, JCVI_ISG_i3_1.0', description=None) | + diff --git a/mixs6/assembly_qual.md b/mixs6/assembly_qual.md new file mode 100644 index 00000000..564db584 --- /dev/null +++ b/mixs6/assembly_qual.md @@ -0,0 +1,42 @@ + +# Slot: assembly_qual + + +The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + +URI: [mixs.vocab:assembly_qual](https://w3id.org/mixs/vocab/assembly_qual) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞assembly_qual](ME_assembly_qual.md) + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | assembly quality | +| **Comments:** | | Expected value: enumeration | +| | | Position: 54.0 | +| **Examples:** | | Example(value='High-quality draft genome', description=None) | + diff --git a/mixs6/assembly_software.md b/mixs6/assembly_software.md new file mode 100644 index 00000000..adeb6672 --- /dev/null +++ b/mixs6/assembly_software.md @@ -0,0 +1,43 @@ + +# Slot: assembly_software + + +Tool(s) used for assembly, including version number and parameters + +URI: [mixs.vocab:assembly_software](https://w3id.org/mixs/vocab/assembly_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞assembly_software](ME_assembly_software.md) + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) + * [MISAG➞assembly_software](MISAG_assembly_software.md) + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | assembly software | +| **Comments:** | | Expected value: name and version of software, parameters used | +| | | Position: 56.0 | +| **Examples:** | | Example(value='metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise', description=None) | + diff --git a/mixs6/atmospheric_data.md b/mixs6/atmospheric_data.md new file mode 100644 index 00000000..a1b96df5 --- /dev/null +++ b/mixs6/atmospheric_data.md @@ -0,0 +1,47 @@ + +# Slot: atmospheric_data + + +Measurement of atmospheric data; can include multiple data + +URI: [mixs.vocab:atmospheric_data](https://w3id.org/mixs/vocab/atmospheric_data) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | atmospheric data | +| **Mappings:** | | MIXS:0001097 | +| **Comments:** | | Expected value: atmospheric data name;measurement value | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='wind speed;9 knots', description=None) | + diff --git a/mixs6/avg_dew_point.md b/mixs6/avg_dew_point.md new file mode 100644 index 00000000..4c259061 --- /dev/null +++ b/mixs6/avg_dew_point.md @@ -0,0 +1,48 @@ + +# Slot: avg_dew_point + + +The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + +URI: [mixs.vocab:avg_dew_point](https://w3id.org/mixs/vocab/avg_dew_point) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | average dew point | +| **Mappings:** | | MIXS:0000141 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 33.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='25.5 degree Celsius', description=None) | + diff --git a/mixs6/avg_occup.md b/mixs6/avg_occup.md new file mode 100644 index 00000000..33442fba --- /dev/null +++ b/mixs6/avg_occup.md @@ -0,0 +1,47 @@ + +# Slot: avg_occup + + +Daily average occupancy of room + +URI: [mixs.vocab:avg_occup](https://w3id.org/mixs/vocab/avg_occup) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | average daily occupancy | +| **Mappings:** | | MIXS:0000775 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 32.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/avg_temp.md b/mixs6/avg_temp.md new file mode 100644 index 00000000..2cf2906d --- /dev/null +++ b/mixs6/avg_temp.md @@ -0,0 +1,48 @@ + +# Slot: avg_temp + + +The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + +URI: [mixs.vocab:avg_temp](https://w3id.org/mixs/vocab/avg_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | average temperature | +| **Mappings:** | | MIXS:0000142 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 34.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='12.5 degree Celsius', description=None) | + diff --git a/mixs6/bac_prod.md b/mixs6/bac_prod.md new file mode 100644 index 00000000..42f01de5 --- /dev/null +++ b/mixs6/bac_prod.md @@ -0,0 +1,48 @@ + +# Slot: bac_prod + + +Bacterial production in the water column measured by isotope uptake + +URI: [mixs.vocab:bac_prod](https://w3id.org/mixs/vocab/bac_prod) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bacterial production | +| **Mappings:** | | MIXS:0000683 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter per day | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='5 milligram per cubic meter per day', description=None) | + diff --git a/mixs6/bac_resp.md b/mixs6/bac_resp.md new file mode 100644 index 00000000..c1731627 --- /dev/null +++ b/mixs6/bac_resp.md @@ -0,0 +1,48 @@ + +# Slot: bac_resp + + +Measurement of bacterial respiration in the water column + +URI: [mixs.vocab:bac_resp](https://w3id.org/mixs/vocab/bac_resp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bacterial respiration | +| **Mappings:** | | MIXS:0000684 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter per day, micromole oxygen per liter per hour | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='300 micromole oxygen per liter per hour', description=None) | + diff --git a/mixs6/bacteria_carb_prod.md b/mixs6/bacteria_carb_prod.md new file mode 100644 index 00000000..f5181c9d --- /dev/null +++ b/mixs6/bacteria_carb_prod.md @@ -0,0 +1,72 @@ + +# Slot: bacteria_carb_prod + + +Measurement of bacterial carbon production + +URI: [mixs.vocab:bacteria_carb_prod](https://w3id.org/mixs/vocab/bacteria_carb_prod) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bacterial carbon production | +| **Mappings:** | | MIXS:0000173 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: nanogram per hour | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='2.53 microgram per liter per hour', description=None) | + diff --git a/mixs6/barometric_press.md b/mixs6/barometric_press.md new file mode 100644 index 00000000..ce02cd17 --- /dev/null +++ b/mixs6/barometric_press.md @@ -0,0 +1,48 @@ + +# Slot: barometric_press + + +Force per unit area exerted against a surface by the weight of air above that surface + +URI: [mixs.vocab:barometric_press](https://w3id.org/mixs/vocab/barometric_press) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | barometric pressure | +| **Mappings:** | | MIXS:0000096 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millibar | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='5 millibar', description=None) | + diff --git a/mixs6/basin.md b/mixs6/basin.md new file mode 100644 index 00000000..03f012aa --- /dev/null +++ b/mixs6/basin.md @@ -0,0 +1,59 @@ + +# Slot: basin + + +Name of the basin (e.g. Campos) + +URI: [mixs.vocab:basin](https://w3id.org/mixs/vocab/basin) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | basin name | +| **Mappings:** | | MIXS:0000290 | +| **Comments:** | | Expected value: name | +| | | Occurrence: 1 | +| | | Position: 3.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bathroom_count.md b/mixs6/bathroom_count.md new file mode 100644 index 00000000..05be8611 --- /dev/null +++ b/mixs6/bathroom_count.md @@ -0,0 +1,47 @@ + +# Slot: bathroom_count + + +The number of bathrooms in the building + +URI: [mixs.vocab:bathroom_count](https://w3id.org/mixs/vocab/bathroom_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bathroom count | +| **Mappings:** | | MIXS:0000776 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 35.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='1', description=None) | + diff --git a/mixs6/bedroom_count.md b/mixs6/bedroom_count.md new file mode 100644 index 00000000..5c375d78 --- /dev/null +++ b/mixs6/bedroom_count.md @@ -0,0 +1,47 @@ + +# Slot: bedroom_count + + +The number of bedrooms in the building + +URI: [mixs.vocab:bedroom_count](https://w3id.org/mixs/vocab/bedroom_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bedroom count | +| **Mappings:** | | MIXS:0000777 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 36.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/benzene.md b/mixs6/benzene.md new file mode 100644 index 00000000..587b4884 --- /dev/null +++ b/mixs6/benzene.md @@ -0,0 +1,60 @@ + +# Slot: benzene + + +Concentration of benzene in the sample + +URI: [mixs.vocab:benzene](https://w3id.org/mixs/vocab/benzene) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | benzene | +| **Mappings:** | | MIXS:0000153 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 81.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bin_param.md b/mixs6/bin_param.md new file mode 100644 index 00000000..df2f6c85 --- /dev/null +++ b/mixs6/bin_param.md @@ -0,0 +1,35 @@ + +# Slot: bin_param + + +The parameters that have been applied during the extraction of genomes from metagenomic datasets + +URI: [mixs.vocab:bin_param](https://w3id.org/mixs/vocab/bin_param) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞bin_param](MIMAG_bin_param.md) + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | binning parameters | +| **Comments:** | | Expected value: enumeration | +| | | Position: 79.0 | +| **Examples:** | | Example(value='coverage and kmer', description=None) | + diff --git a/mixs6/bin_software.md b/mixs6/bin_software.md new file mode 100644 index 00000000..ecf4de12 --- /dev/null +++ b/mixs6/bin_software.md @@ -0,0 +1,35 @@ + +# Slot: bin_software + + +Tool(s) used for the extraction of genomes from metagenomic datasets + +URI: [mixs.vocab:bin_software](https://w3id.org/mixs/vocab/bin_software) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞bin_software](MIMAG_bin_software.md) + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | binning software | +| **Comments:** | | Expected value: enumeration | +| | | Position: 80.0 | +| **Examples:** | | Example(value='concoct and maxbin', description=None) | + diff --git a/mixs6/biochem_oxygen_dem.md b/mixs6/biochem_oxygen_dem.md new file mode 100644 index 00000000..2109a9fd --- /dev/null +++ b/mixs6/biochem_oxygen_dem.md @@ -0,0 +1,48 @@ + +# Slot: biochem_oxygen_dem + + +Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + +URI: [mixs.vocab:biochem_oxygen_dem](https://w3id.org/mixs/vocab/biochem_oxygen_dem) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biochemical oxygen demand | +| **Mappings:** | | MIXS:0000653 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/biocide.md b/mixs6/biocide.md new file mode 100644 index 00000000..a1814000 --- /dev/null +++ b/mixs6/biocide.md @@ -0,0 +1,47 @@ + +# Slot: biocide + + +List of biocides (commercial name of product and supplier) and date of administration + +URI: [mixs.vocab:biocide](https://w3id.org/mixs/vocab/biocide) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biocide administration | +| **Mappings:** | | MIXS:0001011 | +| **Comments:** | | Expected value: name;name;timestamp | +| | | Occurrence: 1 | +| | | Position: 30.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='ALPHA 1427;Baker Hughes;2008-01-23', description=None) | + diff --git a/mixs6/biocide_admin_method.md b/mixs6/biocide_admin_method.md new file mode 100644 index 00000000..8d7fc6bb --- /dev/null +++ b/mixs6/biocide_admin_method.md @@ -0,0 +1,48 @@ + +# Slot: biocide_admin_method + + +Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + +URI: [mixs.vocab:biocide_admin_method](https://w3id.org/mixs/vocab/biocide_admin_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biocide administration method | +| **Mappings:** | | MIXS:0000456 | +| **Comments:** | | Expected value: measurement value;frequency;duration;duration | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 31.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/biol_stat.md b/mixs6/biol_stat.md new file mode 100644 index 00000000..cfb19634 --- /dev/null +++ b/mixs6/biol_stat.md @@ -0,0 +1,59 @@ + +# Slot: biol_stat + + +The level of genome modification. + +URI: [mixs.vocab:biol_stat](https://w3id.org/mixs/vocab/biol_stat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biological status | +| **Mappings:** | | MIXS:0000858 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 2.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='natural', description=None) | + diff --git a/mixs6/biomass.md b/mixs6/biomass.md new file mode 100644 index 00000000..2dda0f85 --- /dev/null +++ b/mixs6/biomass.md @@ -0,0 +1,84 @@ + +# Slot: biomass + + +Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + +URI: [mixs.vocab:biomass](https://w3id.org/mixs/vocab/biomass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biomass | +| **Mappings:** | | MIXS:0000174 | +| **Comments:** | | Expected value: biomass type;measurement value | +| | | Preferred unit: ton, kilogram, gram | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='total;20 gram', description=None) | + diff --git a/mixs6/biotic_regm.md b/mixs6/biotic_regm.md new file mode 100644 index 00000000..52edd831 --- /dev/null +++ b/mixs6/biotic_regm.md @@ -0,0 +1,47 @@ + +# Slot: biotic_regm + + +Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + +URI: [mixs.vocab:biotic_regm](https://w3id.org/mixs/vocab/biotic_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biotic regimen | +| **Mappings:** | | MIXS:0001038 | +| **Comments:** | | Expected value: free text | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='sample inoculated with Rhizobium spp. Culture', description=None) | + diff --git a/mixs6/biotic_relationship.md b/mixs6/biotic_relationship.md new file mode 100644 index 00000000..28d6e304 --- /dev/null +++ b/mixs6/biotic_relationship.md @@ -0,0 +1,38 @@ + +# Slot: biotic_relationship + + +Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + +URI: [mixs.vocab:biotic_relationship](https://w3id.org/mixs/vocab/biotic_relationship) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | observed biotic relationship | +| **Comments:** | | Expected value: enumeration | +| | | Position: 22.0 | +| **Examples:** | | Example(value='free living', description=None) | + diff --git a/mixs6/birth_control.md b/mixs6/birth_control.md new file mode 100644 index 00000000..11ce7227 --- /dev/null +++ b/mixs6/birth_control.md @@ -0,0 +1,47 @@ + +# Slot: birth_control + + +Specification of birth control medication used + +URI: [mixs.vocab:birth_control](https://w3id.org/mixs/vocab/birth_control) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | birth control | +| **Mappings:** | | MIXS:0000286 | +| **Comments:** | | Expected value: medication name | +| | | Occurrence: 1 | +| | | Position: 5.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bishomohopanol.md b/mixs6/bishomohopanol.md new file mode 100644 index 00000000..bd42f065 --- /dev/null +++ b/mixs6/bishomohopanol.md @@ -0,0 +1,72 @@ + +# Slot: bishomohopanol + + +Concentration of bishomohopanol + +URI: [mixs.vocab:bishomohopanol](https://w3id.org/mixs/vocab/bishomohopanol) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bishomohopanol | +| **Mappings:** | | MIXS:0000175 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, microgram per gram | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='14 microgram per liter', description=None) | + diff --git a/mixs6/blood_blood_disord.md b/mixs6/blood_blood_disord.md new file mode 100644 index 00000000..fc8d90f9 --- /dev/null +++ b/mixs6/blood_blood_disord.md @@ -0,0 +1,47 @@ + +# Slot: blood_blood_disord + + +History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + +URI: [mixs.vocab:blood_blood_disord](https://w3id.org/mixs/vocab/blood_blood_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | blood/blood disorder | +| **Mappings:** | | MIXS:0000271 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 32.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bromide.md b/mixs6/bromide.md new file mode 100644 index 00000000..9f5c8174 --- /dev/null +++ b/mixs6/bromide.md @@ -0,0 +1,84 @@ + +# Slot: bromide + + +Concentration of bromide + +URI: [mixs.vocab:bromide](https://w3id.org/mixs/vocab/bromide) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bromide | +| **Mappings:** | | MIXS:0000176 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: parts per million | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.05 parts per million', description=None) | + diff --git a/mixs6/build_docs.md b/mixs6/build_docs.md new file mode 100644 index 00000000..b136634e --- /dev/null +++ b/mixs6/build_docs.md @@ -0,0 +1,47 @@ + +# Slot: build_docs + + +The building design, construction and operation documents + +URI: [mixs.vocab:build_docs](https://w3id.org/mixs/vocab/build_docs) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | design, construction, and operation documents | +| **Mappings:** | | MIXS:0000787 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 50.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='maintenance plans', description=None) | + diff --git a/mixs6/build_occup_type.md b/mixs6/build_occup_type.md new file mode 100644 index 00000000..373b2783 --- /dev/null +++ b/mixs6/build_occup_type.md @@ -0,0 +1,47 @@ + +# Slot: build_occup_type + + +The primary function for which a building or discrete part of a building is intended to be used + +URI: [mixs.vocab:build_occup_type](https://w3id.org/mixs/vocab/build_occup_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | building occupancy type | +| **Mappings:** | | MIXS:0000761 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 9.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='market', description=None) | + diff --git a/mixs6/building_setting.md b/mixs6/building_setting.md new file mode 100644 index 00000000..824f939d --- /dev/null +++ b/mixs6/building_setting.md @@ -0,0 +1,47 @@ + +# Slot: building_setting + + +A location (geography) where a building is set + +URI: [mixs.vocab:building_setting](https://w3id.org/mixs/vocab/building_setting) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | building setting | +| **Mappings:** | | MIXS:0000768 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 20.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='rural', description=None) | + diff --git a/mixs6/built_struc_age.md b/mixs6/built_struc_age.md new file mode 100644 index 00000000..4741bec2 --- /dev/null +++ b/mixs6/built_struc_age.md @@ -0,0 +1,48 @@ + +# Slot: built_struc_age + + +The age of the built structure since construction + +URI: [mixs.vocab:built_struc_age](https://w3id.org/mixs/vocab/built_struc_age) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | built structure age | +| **Mappings:** | | MIXS:0000145 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: year | +| | | Occurrence: 1 | +| | | Position: 37.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='15', description=None) | + diff --git a/mixs6/built_struc_set.md b/mixs6/built_struc_set.md new file mode 100644 index 00000000..9f211918 --- /dev/null +++ b/mixs6/built_struc_set.md @@ -0,0 +1,47 @@ + +# Slot: built_struc_set + + +The characterization of the location of the built structure as high or low human density + +URI: [mixs.vocab:built_struc_set](https://w3id.org/mixs/vocab/built_struc_set) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | built structure setting | +| **Mappings:** | | MIXS:0000778 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 38.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='rural', description=None) | + diff --git a/mixs6/built_struc_type.md b/mixs6/built_struc_type.md new file mode 100644 index 00000000..bbe2df5d --- /dev/null +++ b/mixs6/built_struc_type.md @@ -0,0 +1,47 @@ + +# Slot: built_struc_type + + +A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + +URI: [mixs.vocab:built_struc_type](https://w3id.org/mixs/vocab/built_struc_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | built structure type | +| **Mappings:** | | MIXS:0000721 | +| **Comments:** | | Expected value: free text | +| | | Occurrence: 1 | +| | | Position: 39.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/calcium.md b/mixs6/calcium.md new file mode 100644 index 00000000..05962436 --- /dev/null +++ b/mixs6/calcium.md @@ -0,0 +1,108 @@ + +# Slot: calcium + + +Concentration of calcium in the sample + +URI: [mixs.vocab:calcium](https://w3id.org/mixs/vocab/calcium) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | calcium | +| **Mappings:** | | MIXS:0000432 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, micromole per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 70.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.2 micromole per liter', description=None) | + diff --git a/mixs6/carb_dioxide.md b/mixs6/carb_dioxide.md new file mode 100644 index 00000000..8214f96e --- /dev/null +++ b/mixs6/carb_dioxide.md @@ -0,0 +1,60 @@ + +# Slot: carb_dioxide + + +Carbon dioxide (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:carb_dioxide](https://w3id.org/mixs/vocab/carb_dioxide) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | carbon dioxide | +| **Mappings:** | | MIXS:0000097 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: air, built environment | +| **Examples:** | | Example(value='410 parts per million', description=None) | + diff --git a/mixs6/carb_monoxide.md b/mixs6/carb_monoxide.md new file mode 100644 index 00000000..b24c845a --- /dev/null +++ b/mixs6/carb_monoxide.md @@ -0,0 +1,48 @@ + +# Slot: carb_monoxide + + +Carbon monoxide (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:carb_monoxide](https://w3id.org/mixs/vocab/carb_monoxide) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | carbon monoxide | +| **Mappings:** | | MIXS:0000098 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='0.1 parts per million', description=None) | + diff --git a/mixs6/carb_nitro_ratio.md b/mixs6/carb_nitro_ratio.md new file mode 100644 index 00000000..be2dbb92 --- /dev/null +++ b/mixs6/carb_nitro_ratio.md @@ -0,0 +1,71 @@ + +# Slot: carb_nitro_ratio + + +Ratio of amount or concentrations of carbon to nitrogen + +URI: [mixs.vocab:carb_nitro_ratio](https://w3id.org/mixs/vocab/carb_nitro_ratio) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | carbon/nitrogen ratio | +| **Mappings:** | | MIXS:0000310 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.417361111', description=None) | + diff --git a/mixs6/ceil_area.md b/mixs6/ceil_area.md new file mode 100644 index 00000000..e4442ee3 --- /dev/null +++ b/mixs6/ceil_area.md @@ -0,0 +1,48 @@ + +# Slot: ceil_area + + +The area of the ceiling space within the room + +URI: [mixs.vocab:ceil_area](https://w3id.org/mixs/vocab/ceil_area) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling area | +| **Mappings:** | | MIXS:0000148 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 40.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='25 square meter', description=None) | + diff --git a/mixs6/ceil_cond.md b/mixs6/ceil_cond.md new file mode 100644 index 00000000..d9235b0c --- /dev/null +++ b/mixs6/ceil_cond.md @@ -0,0 +1,47 @@ + +# Slot: ceil_cond + + +The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + +URI: [mixs.vocab:ceil_cond](https://w3id.org/mixs/vocab/ceil_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling condition | +| **Mappings:** | | MIXS:0000779 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 41.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='damaged', description=None) | + diff --git a/mixs6/ceil_finish_mat.md b/mixs6/ceil_finish_mat.md new file mode 100644 index 00000000..2fcb4efe --- /dev/null +++ b/mixs6/ceil_finish_mat.md @@ -0,0 +1,47 @@ + +# Slot: ceil_finish_mat + + +The type of material used to finish a ceiling + +URI: [mixs.vocab:ceil_finish_mat](https://w3id.org/mixs/vocab/ceil_finish_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling finish material | +| **Mappings:** | | MIXS:0000780 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 42.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='stucco', description=None) | + diff --git a/mixs6/ceil_struc.md b/mixs6/ceil_struc.md new file mode 100644 index 00000000..50a00204 --- /dev/null +++ b/mixs6/ceil_struc.md @@ -0,0 +1,47 @@ + +# Slot: ceil_struc + + +The construction format of the ceiling + +URI: [mixs.vocab:ceil_struc](https://w3id.org/mixs/vocab/ceil_struc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling structure | +| **Mappings:** | | MIXS:0000782 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 44.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='concrete', description=None) | + diff --git a/mixs6/ceil_texture.md b/mixs6/ceil_texture.md new file mode 100644 index 00000000..2a3b318e --- /dev/null +++ b/mixs6/ceil_texture.md @@ -0,0 +1,47 @@ + +# Slot: ceil_texture + + +The feel, appearance, or consistency of a ceiling surface + +URI: [mixs.vocab:ceil_texture](https://w3id.org/mixs/vocab/ceil_texture) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling texture | +| **Mappings:** | | MIXS:0000783 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 45.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='popcorn', description=None) | + diff --git a/mixs6/ceil_thermal_mass.md b/mixs6/ceil_thermal_mass.md new file mode 100644 index 00000000..b864db5e --- /dev/null +++ b/mixs6/ceil_thermal_mass.md @@ -0,0 +1,48 @@ + +# Slot: ceil_thermal_mass + + +The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + +URI: [mixs.vocab:ceil_thermal_mass](https://w3id.org/mixs/vocab/ceil_thermal_mass) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling thermal mass | +| **Mappings:** | | MIXS:0000143 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: joule per degree Celsius | +| | | Occurrence: 1 | +| | | Position: 46.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ceil_type.md b/mixs6/ceil_type.md new file mode 100644 index 00000000..3604f2c1 --- /dev/null +++ b/mixs6/ceil_type.md @@ -0,0 +1,47 @@ + +# Slot: ceil_type + + +The type of ceiling according to the ceiling's appearance or construction + +URI: [mixs.vocab:ceil_type](https://w3id.org/mixs/vocab/ceil_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling type | +| **Mappings:** | | MIXS:0000784 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 47.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='coffered', description=None) | + diff --git a/mixs6/ceil_water_mold.md b/mixs6/ceil_water_mold.md new file mode 100644 index 00000000..be453c7a --- /dev/null +++ b/mixs6/ceil_water_mold.md @@ -0,0 +1,47 @@ + +# Slot: ceil_water_mold + + +Signs of the presence of mold or mildew on the ceiling + +URI: [mixs.vocab:ceil_water_mold](https://w3id.org/mixs/vocab/ceil_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling signs of water/mold | +| **Mappings:** | | MIXS:0000781 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 43.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='presence of mold visible', description=None) | + diff --git a/mixs6/chem_administration.md b/mixs6/chem_administration.md new file mode 100644 index 00000000..68007280 --- /dev/null +++ b/mixs6/chem_administration.md @@ -0,0 +1,191 @@ + +# Slot: chem_administration + + +List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + +URI: [mixs.vocab:chem_administration](https://w3id.org/mixs/vocab/chem_administration) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical administration | +| **Mappings:** | | MIXS:0000751 | +| **Comments:** | | Expected value: CHEBI;timestamp | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 13 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='agar [CHEBI:2509];2018-05-11T20:00Z', description=None) | + diff --git a/mixs6/chem_mutagen.md b/mixs6/chem_mutagen.md new file mode 100644 index 00000000..ef23a9d2 --- /dev/null +++ b/mixs6/chem_mutagen.md @@ -0,0 +1,48 @@ + +# Slot: chem_mutagen + + +Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + +URI: [mixs.vocab:chem_mutagen](https://w3id.org/mixs/vocab/chem_mutagen) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical mutagen | +| **Mappings:** | | MIXS:0000555 | +| **Comments:** | | Expected value: mutagen name;mutagen amount;treatment interval and duration | +| | | Preferred unit: milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/chem_oxygen_dem.md b/mixs6/chem_oxygen_dem.md new file mode 100644 index 00000000..f070d4b2 --- /dev/null +++ b/mixs6/chem_oxygen_dem.md @@ -0,0 +1,48 @@ + +# Slot: chem_oxygen_dem + + +A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + +URI: [mixs.vocab:chem_oxygen_dem](https://w3id.org/mixs/vocab/chem_oxygen_dem) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical oxygen demand | +| **Mappings:** | | MIXS:0000656 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/chem_treatment.md b/mixs6/chem_treatment.md new file mode 100644 index 00000000..f01e54ec --- /dev/null +++ b/mixs6/chem_treatment.md @@ -0,0 +1,47 @@ + +# Slot: chem_treatment + + +List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + +URI: [mixs.vocab:chem_treatment](https://w3id.org/mixs/vocab/chem_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical treatment | +| **Mappings:** | | MIXS:0001012 | +| **Comments:** | | Expected value: name;name;timestamp | +| | | Occurrence: 1 | +| | | Position: 32.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='ACCENT 1125;DOW;2010-11-17', description=None) | + diff --git a/mixs6/chem_treatment_method.md b/mixs6/chem_treatment_method.md new file mode 100644 index 00000000..3c207a7b --- /dev/null +++ b/mixs6/chem_treatment_method.md @@ -0,0 +1,48 @@ + +# Slot: chem_treatment_method + + +Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + +URI: [mixs.vocab:chem_treatment_method](https://w3id.org/mixs/vocab/chem_treatment_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical treatment method | +| **Mappings:** | | MIXS:0000457 | +| **Comments:** | | Expected value: measurement value;frequency;duration;duration | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 33.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/chimera_check.md b/mixs6/chimera_check.md new file mode 100644 index 00000000..10ead016 --- /dev/null +++ b/mixs6/chimera_check.md @@ -0,0 +1,35 @@ + +# Slot: chimera_check + + +A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + +URI: [mixs.vocab:chimera_check](https://w3id.org/mixs/vocab/chimera_check) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chimera check | +| **Comments:** | | Expected value: name and version of software, parameters used | +| | | Position: 52.0 | +| **Examples:** | | Example(value='uchime;v4.1;default parameters', description=None) | + diff --git a/mixs6/chloride.md b/mixs6/chloride.md new file mode 100644 index 00000000..10657fad --- /dev/null +++ b/mixs6/chloride.md @@ -0,0 +1,108 @@ + +# Slot: chloride + + +Concentration of chloride in the sample + +URI: [mixs.vocab:chloride](https://w3id.org/mixs/vocab/chloride) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chloride | +| **Mappings:** | | MIXS:0000429 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 67.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5000 milligram per liter', description=None) | + diff --git a/mixs6/chlorophyll.md b/mixs6/chlorophyll.md new file mode 100644 index 00000000..3e0c1100 --- /dev/null +++ b/mixs6/chlorophyll.md @@ -0,0 +1,84 @@ + +# Slot: chlorophyll + + +Concentration of chlorophyll + +URI: [mixs.vocab:chlorophyll](https://w3id.org/mixs/vocab/chlorophyll) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chlorophyll | +| **Mappings:** | | MIXS:0000177 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter, microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5 milligram per cubic meter', description=None) | + diff --git a/mixs6/climate_environment.md b/mixs6/climate_environment.md new file mode 100644 index 00000000..44bd69d8 --- /dev/null +++ b/mixs6/climate_environment.md @@ -0,0 +1,47 @@ + +# Slot: climate_environment + + +Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + +URI: [mixs.vocab:climate_environment](https://w3id.org/mixs/vocab/climate_environment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | climate environment | +| **Mappings:** | | MIXS:0001040 | +| **Comments:** | | Expected value: climate name;treatment interval and duration | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/collection_date.md b/mixs6/collection_date.md new file mode 100644 index 00000000..c91d5e8c --- /dev/null +++ b/mixs6/collection_date.md @@ -0,0 +1,248 @@ + +# Slot: collection_date + + +The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + +URI: [mixs.vocab:collection_date](https://w3id.org/mixs/vocab/collection_date) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + * [ME➞collection_date](ME_collection_date.md) + * [MIGS bacteria➞collection_date](MIGS_bacteria_collection_date.md) + * [MIGS eukaryote➞collection_date](MIGS_eukaryote_collection_date.md) + * [MIGS org➞collection_date](MIGS_org_collection_date.md) + * [MIGS plant➞collection_date](MIGS_plant_collection_date.md) + * [MIGS virus➞collection_date](MIGS_virus_collection_date.md) + * [MIMAG➞collection_date](MIMAG_collection_date.md) + * [MIMARKS specimen➞collection_date](MIMARKS_specimen_collection_date.md) + * [MIMARKS survey➞collection_date](MIMARKS_survey_collection_date.md) + * [MISAG➞collection_date](MISAG_collection_date.md) + * [MIUVIG➞collection_date](MIUVIG_collection_date.md) + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | collection date | +| **Comments:** | | Expected value: date and time | +| | | Position: 9.0 | +| **Examples:** | | Example(value='2018-05-11T10:00:00+01:00', description=None) | + diff --git a/mixs6/compl_appr.md b/mixs6/compl_appr.md new file mode 100644 index 00000000..ed7fed50 --- /dev/null +++ b/mixs6/compl_appr.md @@ -0,0 +1,36 @@ + +# Slot: compl_appr + + +The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + +URI: [mixs.vocab:compl_appr](https://w3id.org/mixs/vocab/compl_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) + * [MISAG➞compl_appr](MISAG_compl_appr.md) + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | completeness approach | +| **Comments:** | | Expected value: enumeration | +| | | Position: 69.0 | +| **Examples:** | | Example(value='other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)', description=None) | + diff --git a/mixs6/compl_score.md b/mixs6/compl_score.md new file mode 100644 index 00000000..3ed0b69d --- /dev/null +++ b/mixs6/compl_score.md @@ -0,0 +1,41 @@ + +# Slot: compl_score + + +Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + +URI: [mixs.vocab:compl_score](https://w3id.org/mixs/vocab/compl_score) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) + * [MIGS org➞compl_score](MIGS_org_compl_score.md) + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) + * [MIMAG➞compl_score](MIMAG_compl_score.md) + * [MISAG➞compl_score](MISAG_compl_score.md) + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | completeness score | +| **Comments:** | | Expected value: quality;percent completeness | +| | | Position: 67.0 | +| **Examples:** | | Example(value='med;60%', description=None) | + diff --git a/mixs6/compl_software.md b/mixs6/compl_software.md new file mode 100644 index 00000000..ecff4e69 --- /dev/null +++ b/mixs6/compl_software.md @@ -0,0 +1,41 @@ + +# Slot: compl_software + + +Tools used for completion estimate, i.e. checkm, anvi'o, busco + +URI: [mixs.vocab:compl_software](https://w3id.org/mixs/vocab/compl_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) + * [MIGS org➞compl_software](MIGS_org_compl_software.md) + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) + * [MIMAG➞compl_software](MIMAG_compl_software.md) + * [MISAG➞compl_software](MISAG_compl_software.md) + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | completeness software | +| **Comments:** | | Expected value: names and versions of software(s) used | +| | | Position: 68.0 | +| **Examples:** | | Example(value='checkm', description=None) | + diff --git a/mixs6/conduc.md b/mixs6/conduc.md new file mode 100644 index 00000000..90a031e4 --- /dev/null +++ b/mixs6/conduc.md @@ -0,0 +1,48 @@ + +# Slot: conduc + + +Electrical conductivity of water + +URI: [mixs.vocab:conduc](https://w3id.org/mixs/vocab/conduc) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | conductivity | +| **Mappings:** | | MIXS:0000692 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milliSiemens per centimeter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='10 milliSiemens per centimeter', description=None) | + diff --git a/mixs6/contam_score.md b/mixs6/contam_score.md new file mode 100644 index 00000000..e7b0db8e --- /dev/null +++ b/mixs6/contam_score.md @@ -0,0 +1,35 @@ + +# Slot: contam_score + + +The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + +URI: [mixs.vocab:contam_score](https://w3id.org/mixs/vocab/contam_score) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞contam_score](MIMAG_contam_score.md) + * [MISAG➞contam_score](MISAG_contam_score.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | contamination score | +| **Comments:** | | Expected value: value | +| | | Position: 70.0 | +| **Examples:** | | Example(value='1%', description=None) | + diff --git a/mixs6/contam_screen_input.md b/mixs6/contam_screen_input.md new file mode 100644 index 00000000..8ceeff54 --- /dev/null +++ b/mixs6/contam_screen_input.md @@ -0,0 +1,35 @@ + +# Slot: contam_screen_input + + +The type of sequence data used as input + +URI: [mixs.vocab:contam_screen_input](https://w3id.org/mixs/vocab/contam_screen_input) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | contamination screening input | +| **Comments:** | | Expected value: enumeration | +| | | Position: 71.0 | +| **Examples:** | | Example(value='contigs', description=None) | + diff --git a/mixs6/contam_screen_param.md b/mixs6/contam_screen_param.md new file mode 100644 index 00000000..e8910596 --- /dev/null +++ b/mixs6/contam_screen_param.md @@ -0,0 +1,35 @@ + +# Slot: contam_screen_param + + +Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + +URI: [mixs.vocab:contam_screen_param](https://w3id.org/mixs/vocab/contam_screen_param) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | contamination screening parameters | +| **Comments:** | | Expected value: enumeration;value or name | +| | | Position: 72.0 | +| **Examples:** | | Example(value='kmer', description=None) | + diff --git a/mixs6/cool_syst_id.md b/mixs6/cool_syst_id.md new file mode 100644 index 00000000..be9b932f --- /dev/null +++ b/mixs6/cool_syst_id.md @@ -0,0 +1,47 @@ + +# Slot: cool_syst_id + + +The cooling system identifier + +URI: [mixs.vocab:cool_syst_id](https://w3id.org/mixs/vocab/cool_syst_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | cooling system identifier | +| **Mappings:** | | MIXS:0000785 | +| **Comments:** | | Expected value: unique identifier | +| | | Occurrence: 1 | +| | | Position: 48.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='12345', description=None) | + diff --git a/mixs6/core_field.md b/mixs6/core_field.md new file mode 100644 index 00000000..9e460f92 --- /dev/null +++ b/mixs6/core_field.md @@ -0,0 +1,21 @@ + +# Slot: core_field + + +basic fields + +URI: [mixs.vocab:core_field](https://w3id.org/mixs/vocab/core_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + +## Used by + diff --git a/mixs6/crop_rotation.md b/mixs6/crop_rotation.md new file mode 100644 index 00000000..c99fd296 --- /dev/null +++ b/mixs6/crop_rotation.md @@ -0,0 +1,47 @@ + +# Slot: crop_rotation + + +Whether or not crop is rotated, and if yes, rotation schedule + +URI: [mixs.vocab:crop_rotation](https://w3id.org/mixs/vocab/crop_rotation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/crop rotation | +| **Mappings:** | | MIXS:0000318 | +| **Comments:** | | Expected value: crop rotation status;schedule | +| | | Occurrence: 1 | +| | | Position: 6.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='yes;R2/2017-01-01/2018-12-31/P6M', description=None) | + diff --git a/mixs6/cult_root_med.md b/mixs6/cult_root_med.md new file mode 100644 index 00000000..9b4a61af --- /dev/null +++ b/mixs6/cult_root_med.md @@ -0,0 +1,47 @@ + +# Slot: cult_root_med + + +Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + +URI: [mixs.vocab:cult_root_med](https://w3id.org/mixs/vocab/cult_root_med) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | culture rooting medium | +| **Mappings:** | | MIXS:0001041 | +| **Comments:** | | Expected value: name, PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='http://himedialabs.com/TD/PT158.pdf', description=None) | + diff --git a/mixs6/cur_land_use.md b/mixs6/cur_land_use.md new file mode 100644 index 00000000..18cb07b6 --- /dev/null +++ b/mixs6/cur_land_use.md @@ -0,0 +1,47 @@ + +# Slot: cur_land_use + + +Present state of sample site + +URI: [mixs.vocab:cur_land_use](https://w3id.org/mixs/vocab/cur_land_use) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | current land use | +| **Mappings:** | | MIXS:0001080 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='conifers', description=None) | + diff --git a/mixs6/cur_vegetation.md b/mixs6/cur_vegetation.md new file mode 100644 index 00000000..8b64c72f --- /dev/null +++ b/mixs6/cur_vegetation.md @@ -0,0 +1,47 @@ + +# Slot: cur_vegetation + + +Vegetation classification from one or more standard classification systems, or agricultural crop + +URI: [mixs.vocab:cur_vegetation](https://w3id.org/mixs/vocab/cur_vegetation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | current vegetation | +| **Mappings:** | | MIXS:0000312 | +| **Comments:** | | Expected value: current vegetation type | +| | | Occurrence: 1 | +| | | Position: 2.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/cur_vegetation_meth.md b/mixs6/cur_vegetation_meth.md new file mode 100644 index 00000000..d11c034a --- /dev/null +++ b/mixs6/cur_vegetation_meth.md @@ -0,0 +1,47 @@ + +# Slot: cur_vegetation_meth + + +Reference or method used in vegetation classification + +URI: [mixs.vocab:cur_vegetation_meth](https://w3id.org/mixs/vocab/cur_vegetation_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | current vegetation method | +| **Mappings:** | | MIXS:0000314 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 3.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/date_last_rain.md b/mixs6/date_last_rain.md new file mode 100644 index 00000000..6ea78be7 --- /dev/null +++ b/mixs6/date_last_rain.md @@ -0,0 +1,47 @@ + +# Slot: date_last_rain + + +The date of the last time it rained + +URI: [mixs.vocab:date_last_rain](https://w3id.org/mixs/vocab/date_last_rain) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | date last rain | +| **Mappings:** | | MIXS:0000786 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 49.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2018-05-11:T14:30Z', description=None) | + diff --git a/mixs6/decontam_software.md b/mixs6/decontam_software.md new file mode 100644 index 00000000..ccbc9c0c --- /dev/null +++ b/mixs6/decontam_software.md @@ -0,0 +1,35 @@ + +# Slot: decontam_software + + +Tool(s) used in contamination screening + +URI: [mixs.vocab:decontam_software](https://w3id.org/mixs/vocab/decontam_software) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) + * [MISAG➞decontam_software](MISAG_decontam_software.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | decontamination software | +| **Comments:** | | Expected value: enumeration | +| | | Position: 73.0 | +| **Examples:** | | Example(value="anvi'o", description=None) | + diff --git a/mixs6/density.md b/mixs6/density.md new file mode 100644 index 00000000..86c203db --- /dev/null +++ b/mixs6/density.md @@ -0,0 +1,96 @@ + +# Slot: density + + +Density of the sample, which is its mass per unit volume (aka volumetric mass density) + +URI: [mixs.vocab:density](https://w3id.org/mixs/vocab/density) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | density | +| **Mappings:** | | MIXS:0000435 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per cubic meter, gram per cubic centimeter | +| | | Occurrence: 1 | +| | | Position: 77.0 | +| | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1000 kilogram per cubic meter', description=None) | + diff --git a/mixs6/depos_env.md b/mixs6/depos_env.md new file mode 100644 index 00000000..b7114ecc --- /dev/null +++ b/mixs6/depos_env.md @@ -0,0 +1,59 @@ + +# Slot: depos_env + + +Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:depos_env](https://w3id.org/mixs/vocab/depos_env) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | depositional environment | +| **Mappings:** | | MIXS:0000992 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 13.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Continental - Alluvial', description=None) | + diff --git a/mixs6/depth.md b/mixs6/depth.md new file mode 100644 index 00000000..5d491db8 --- /dev/null +++ b/mixs6/depth.md @@ -0,0 +1,239 @@ + +# Slot: depth + + +The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + +URI: [mixs.vocab:depth](https://w3id.org/mixs/vocab/depth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | geographic location (depth) | +| **Comments:** | | Expected value: - | +| | | Position: 6.0 | +| | | This field is used in: 8 packages: host-associated, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/63 | + diff --git a/mixs6/dermatology_disord.md b/mixs6/dermatology_disord.md new file mode 100644 index 00000000..e6df0d9c --- /dev/null +++ b/mixs6/dermatology_disord.md @@ -0,0 +1,47 @@ + +# Slot: dermatology_disord + + +History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + +URI: [mixs.vocab:dermatology_disord](https://w3id.org/mixs/vocab/dermatology_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dermatology disorder | +| **Mappings:** | | MIXS:0000284 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: human-skin | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/detec_type.md b/mixs6/detec_type.md new file mode 100644 index 00000000..ee2ab90c --- /dev/null +++ b/mixs6/detec_type.md @@ -0,0 +1,34 @@ + +# Slot: detec_type + + +Type of UViG detection + +URI: [mixs.vocab:detec_type](https://w3id.org/mixs/vocab/detec_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | detection type | +| **Comments:** | | Expected value: enumeration | +| | | Position: 86.0 | +| **Examples:** | | Example(value='independent sequence (UViG)', description=None) | + diff --git a/mixs6/dew_point.md b/mixs6/dew_point.md new file mode 100644 index 00000000..9a5f0ba4 --- /dev/null +++ b/mixs6/dew_point.md @@ -0,0 +1,48 @@ + +# Slot: dew_point + + +The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + +URI: [mixs.vocab:dew_point](https://w3id.org/mixs/vocab/dew_point) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dew point | +| **Mappings:** | | MIXS:0000129 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 11.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='22 degree Celsius', description=None) | + diff --git a/mixs6/diet_last_six_month.md b/mixs6/diet_last_six_month.md new file mode 100644 index 00000000..54b13d3b --- /dev/null +++ b/mixs6/diet_last_six_month.md @@ -0,0 +1,47 @@ + +# Slot: diet_last_six_month + + +Specification of major diet changes in the last six months, if yes the change should be specified + +URI: [mixs.vocab:diet_last_six_month](https://w3id.org/mixs/vocab/diet_last_six_month) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | major diet change in last six months | +| **Mappings:** | | MIXS:0000266 | +| **Comments:** | | Expected value: diet change;current diet | +| | | Occurrence: 1 | +| | | Position: 21.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes;vegetarian diet', description=None) | + diff --git a/mixs6/diether_lipids.md b/mixs6/diether_lipids.md new file mode 100644 index 00000000..e0f0b537 --- /dev/null +++ b/mixs6/diether_lipids.md @@ -0,0 +1,84 @@ + +# Slot: diether_lipids + + +Concentration of diether lipids; can include multiple types of diether lipids + +URI: [mixs.vocab:diether_lipids](https://w3id.org/mixs/vocab/diether_lipids) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | diether lipids | +| **Mappings:** | | MIXS:0000178 | +| **Comments:** | | Expected value: diether lipid name;measurement value | +| | | Preferred unit: nanogram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.2 nanogram per liter', description=None) | + diff --git a/mixs6/diss_carb_dioxide.md b/mixs6/diss_carb_dioxide.md new file mode 100644 index 00000000..5a9262b8 --- /dev/null +++ b/mixs6/diss_carb_dioxide.md @@ -0,0 +1,108 @@ + +# Slot: diss_carb_dioxide + + +Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + +URI: [mixs.vocab:diss_carb_dioxide](https://w3id.org/mixs/vocab/diss_carb_dioxide) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved carbon dioxide | +| **Mappings:** | | MIXS:0000436 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 78.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5 milligram per liter', description=None) | + diff --git a/mixs6/diss_hydrogen.md b/mixs6/diss_hydrogen.md new file mode 100644 index 00000000..34bd6e41 --- /dev/null +++ b/mixs6/diss_hydrogen.md @@ -0,0 +1,84 @@ + +# Slot: diss_hydrogen + + +Concentration of dissolved hydrogen + +URI: [mixs.vocab:diss_hydrogen](https://w3id.org/mixs/vocab/diss_hydrogen) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved hydrogen | +| **Mappings:** | | MIXS:0000179 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.3 micromole per liter', description=None) | + diff --git a/mixs6/diss_inorg_carb.md b/mixs6/diss_inorg_carb.md new file mode 100644 index 00000000..9da0bd53 --- /dev/null +++ b/mixs6/diss_inorg_carb.md @@ -0,0 +1,108 @@ + +# Slot: diss_inorg_carb + + +Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + +URI: [mixs.vocab:diss_inorg_carb](https://w3id.org/mixs/vocab/diss_inorg_carb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved inorganic carbon | +| **Mappings:** | | MIXS:0000434 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 73.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='2059 micromole per kilogram', description=None) | + diff --git a/mixs6/diss_inorg_nitro.md b/mixs6/diss_inorg_nitro.md new file mode 100644 index 00000000..a796a8dd --- /dev/null +++ b/mixs6/diss_inorg_nitro.md @@ -0,0 +1,48 @@ + +# Slot: diss_inorg_nitro + + +Concentration of dissolved inorganic nitrogen + +URI: [mixs.vocab:diss_inorg_nitro](https://w3id.org/mixs/vocab/diss_inorg_nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved inorganic nitrogen | +| **Mappings:** | | MIXS:0000698 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='761 micromole per liter', description=None) | + diff --git a/mixs6/diss_inorg_phosp.md b/mixs6/diss_inorg_phosp.md new file mode 100644 index 00000000..b240d1f0 --- /dev/null +++ b/mixs6/diss_inorg_phosp.md @@ -0,0 +1,72 @@ + +# Slot: diss_inorg_phosp + + +Concentration of dissolved inorganic phosphorus in the sample + +URI: [mixs.vocab:diss_inorg_phosp](https://w3id.org/mixs/vocab/diss_inorg_phosp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved inorganic phosphorus | +| **Mappings:** | | MIXS:0000106 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 74.0 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | +| **Examples:** | | Example(value='56.5 micromole per liter', description=None) | + diff --git a/mixs6/diss_iron.md b/mixs6/diss_iron.md new file mode 100644 index 00000000..a455f06d --- /dev/null +++ b/mixs6/diss_iron.md @@ -0,0 +1,60 @@ + +# Slot: diss_iron + + +Concentration of dissolved iron in the sample + +URI: [mixs.vocab:diss_iron](https://w3id.org/mixs/vocab/diss_iron) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved iron | +| **Mappings:** | | MIXS:0000139 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 65.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/diss_org_carb.md b/mixs6/diss_org_carb.md new file mode 100644 index 00000000..96f74502 --- /dev/null +++ b/mixs6/diss_org_carb.md @@ -0,0 +1,96 @@ + +# Slot: diss_org_carb + + +Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + +URI: [mixs.vocab:diss_org_carb](https://w3id.org/mixs/vocab/diss_org_carb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved organic carbon | +| **Mappings:** | | MIXS:0000433 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 72.0 | +| | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='197 micromole per liter', description=None) | + diff --git a/mixs6/diss_org_nitro.md b/mixs6/diss_org_nitro.md new file mode 100644 index 00000000..a11e8452 --- /dev/null +++ b/mixs6/diss_org_nitro.md @@ -0,0 +1,84 @@ + +# Slot: diss_org_nitro + + +Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + +URI: [mixs.vocab:diss_org_nitro](https://w3id.org/mixs/vocab/diss_org_nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved organic nitrogen | +| **Mappings:** | | MIXS:0000162 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.05 micromole per liter', description=None) | + diff --git a/mixs6/diss_oxygen.md b/mixs6/diss_oxygen.md new file mode 100644 index 00000000..8907fe52 --- /dev/null +++ b/mixs6/diss_oxygen.md @@ -0,0 +1,84 @@ + +# Slot: diss_oxygen + + +Concentration of dissolved oxygen + +URI: [mixs.vocab:diss_oxygen](https://w3id.org/mixs/vocab/diss_oxygen) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved oxygen | +| **Mappings:** | | MIXS:0000119 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per kilogram, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='175 micromole per kilogram', description=None) | + diff --git a/mixs6/diss_oxygen_fluid.md b/mixs6/diss_oxygen_fluid.md new file mode 100644 index 00000000..d95cf666 --- /dev/null +++ b/mixs6/diss_oxygen_fluid.md @@ -0,0 +1,60 @@ + +# Slot: diss_oxygen_fluid + + +Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + +URI: [mixs.vocab:diss_oxygen_fluid](https://w3id.org/mixs/vocab/diss_oxygen_fluid) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved oxygen in fluids | +| **Mappings:** | | MIXS:0000438 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per kilogram, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 79.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/dominant_hand.md b/mixs6/dominant_hand.md new file mode 100644 index 00000000..ee4c839c --- /dev/null +++ b/mixs6/dominant_hand.md @@ -0,0 +1,47 @@ + +# Slot: dominant_hand + + +Dominant hand of the subject + +URI: [mixs.vocab:dominant_hand](https://w3id.org/mixs/vocab/dominant_hand) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dominant hand | +| **Mappings:** | | MIXS:0000944 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 3.0 | +| | | This field is used uniquely in: human-skin | +| **Examples:** | | Example(value='right', description=None) | + diff --git a/mixs6/door_comp_type.md b/mixs6/door_comp_type.md new file mode 100644 index 00000000..89c04ff9 --- /dev/null +++ b/mixs6/door_comp_type.md @@ -0,0 +1,47 @@ + +# Slot: door_comp_type + + +The composite type of the door + +URI: [mixs.vocab:door_comp_type](https://w3id.org/mixs/vocab/door_comp_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type, composite | +| **Mappings:** | | MIXS:0000795 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 59.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='revolving', description=None) | + diff --git a/mixs6/door_cond.md b/mixs6/door_cond.md new file mode 100644 index 00000000..ae161f20 --- /dev/null +++ b/mixs6/door_cond.md @@ -0,0 +1,47 @@ + +# Slot: door_cond + + +The phsical condition of the door + +URI: [mixs.vocab:door_cond](https://w3id.org/mixs/vocab/door_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door condition | +| **Mappings:** | | MIXS:0000788 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 52.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/door_direct.md b/mixs6/door_direct.md new file mode 100644 index 00000000..96996585 --- /dev/null +++ b/mixs6/door_direct.md @@ -0,0 +1,47 @@ + +# Slot: door_direct + + +The direction the door opens + +URI: [mixs.vocab:door_direct](https://w3id.org/mixs/vocab/door_direct) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door direction of opening | +| **Mappings:** | | MIXS:0000789 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 53.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='inward', description=None) | + diff --git a/mixs6/door_loc.md b/mixs6/door_loc.md new file mode 100644 index 00000000..29c3a1c7 --- /dev/null +++ b/mixs6/door_loc.md @@ -0,0 +1,47 @@ + +# Slot: door_loc + + +The relative location of the door in the room + +URI: [mixs.vocab:door_loc](https://w3id.org/mixs/vocab/door_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door location | +| **Mappings:** | | MIXS:0000790 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 54.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='north', description=None) | + diff --git a/mixs6/door_mat.md b/mixs6/door_mat.md new file mode 100644 index 00000000..41db1463 --- /dev/null +++ b/mixs6/door_mat.md @@ -0,0 +1,47 @@ + +# Slot: door_mat + + +The material the door is composed of + +URI: [mixs.vocab:door_mat](https://w3id.org/mixs/vocab/door_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door material | +| **Mappings:** | | MIXS:0000791 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 55.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/door_move.md b/mixs6/door_move.md new file mode 100644 index 00000000..c00ae483 --- /dev/null +++ b/mixs6/door_move.md @@ -0,0 +1,47 @@ + +# Slot: door_move + + +The type of movement of the door + +URI: [mixs.vocab:door_move](https://w3id.org/mixs/vocab/door_move) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door movement | +| **Mappings:** | | MIXS:0000792 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 56.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='swinging', description=None) | + diff --git a/mixs6/door_size.md b/mixs6/door_size.md new file mode 100644 index 00000000..57726e98 --- /dev/null +++ b/mixs6/door_size.md @@ -0,0 +1,48 @@ + +# Slot: door_size + + +The size of the door + +URI: [mixs.vocab:door_size](https://w3id.org/mixs/vocab/door_size) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door area or size | +| **Mappings:** | | MIXS:0000158 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 51.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2.5 square meter', description=None) | + diff --git a/mixs6/door_type.md b/mixs6/door_type.md new file mode 100644 index 00000000..75f9558c --- /dev/null +++ b/mixs6/door_type.md @@ -0,0 +1,47 @@ + +# Slot: door_type + + +The type of door material + +URI: [mixs.vocab:door_type](https://w3id.org/mixs/vocab/door_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type | +| **Mappings:** | | MIXS:0000794 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 58.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wooden', description=None) | + diff --git a/mixs6/door_type_metal.md b/mixs6/door_type_metal.md new file mode 100644 index 00000000..4921fda2 --- /dev/null +++ b/mixs6/door_type_metal.md @@ -0,0 +1,47 @@ + +# Slot: door_type_metal + + +The type of metal door + +URI: [mixs.vocab:door_type_metal](https://w3id.org/mixs/vocab/door_type_metal) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type, metal | +| **Mappings:** | | MIXS:0000796 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 60.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='hollow', description=None) | + diff --git a/mixs6/door_type_wood.md b/mixs6/door_type_wood.md new file mode 100644 index 00000000..75aa86cb --- /dev/null +++ b/mixs6/door_type_wood.md @@ -0,0 +1,47 @@ + +# Slot: door_type_wood + + +The type of wood door + +URI: [mixs.vocab:door_type_wood](https://w3id.org/mixs/vocab/door_type_wood) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type, wood | +| **Mappings:** | | MIXS:0000797 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 61.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='battened', description=None) | + diff --git a/mixs6/door_water_mold.md b/mixs6/door_water_mold.md new file mode 100644 index 00000000..cb9361ee --- /dev/null +++ b/mixs6/door_water_mold.md @@ -0,0 +1,47 @@ + +# Slot: door_water_mold + + +Signs of the presence of mold or mildew on a door + +URI: [mixs.vocab:door_water_mold](https://w3id.org/mixs/vocab/door_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door signs of water/mold | +| **Mappings:** | | MIXS:0000793 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 57.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='presence of mold visible', description=None) | + diff --git a/mixs6/douche.md b/mixs6/douche.md new file mode 100644 index 00000000..2784edb7 --- /dev/null +++ b/mixs6/douche.md @@ -0,0 +1,47 @@ + +# Slot: douche + + +Date of most recent douche + +URI: [mixs.vocab:douche](https://w3id.org/mixs/vocab/douche) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | douche | +| **Mappings:** | | MIXS:0000967 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 4.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/down_par.md b/mixs6/down_par.md new file mode 100644 index 00000000..5b49fda7 --- /dev/null +++ b/mixs6/down_par.md @@ -0,0 +1,48 @@ + +# Slot: down_par + + +Visible waveband radiance and irradiance measurements in the water column + +URI: [mixs.vocab:down_par](https://w3id.org/mixs/vocab/down_par) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | downward PAR | +| **Mappings:** | | MIXS:0000703 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microEinstein per square meter per second, microEinstein per square centimeter per second | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='28.71 microEinstein per square meter per second', description=None) | + diff --git a/mixs6/drainage_class.md b/mixs6/drainage_class.md new file mode 100644 index 00000000..1d381095 --- /dev/null +++ b/mixs6/drainage_class.md @@ -0,0 +1,47 @@ + +# Slot: drainage_class + + +Drainage classification from a standard system such as the USDA system + +URI: [mixs.vocab:drainage_class](https://w3id.org/mixs/vocab/drainage_class) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | drainage classification | +| **Mappings:** | | MIXS:0001085 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 34.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='well', description=None) | + diff --git a/mixs6/drawings.md b/mixs6/drawings.md new file mode 100644 index 00000000..550ee91c --- /dev/null +++ b/mixs6/drawings.md @@ -0,0 +1,47 @@ + +# Slot: drawings + + +The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + +URI: [mixs.vocab:drawings](https://w3id.org/mixs/vocab/drawings) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | drawings | +| **Mappings:** | | MIXS:0000798 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 62.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='sketch', description=None) | + diff --git a/mixs6/drug_usage.md b/mixs6/drug_usage.md new file mode 100644 index 00000000..1ff28ecf --- /dev/null +++ b/mixs6/drug_usage.md @@ -0,0 +1,47 @@ + +# Slot: drug_usage + + +Any drug used by subject and the frequency of usage; can include multiple drugs used + +URI: [mixs.vocab:drug_usage](https://w3id.org/mixs/vocab/drug_usage) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | drug usage | +| **Mappings:** | | MIXS:0000894 | +| **Comments:** | | Expected value: drug name;frequency | +| | | Occurrence: m | +| | | Position: 19.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='Lipitor;2/day', description=None) | + diff --git a/mixs6/efficiency_percent.md b/mixs6/efficiency_percent.md new file mode 100644 index 00000000..3f457c67 --- /dev/null +++ b/mixs6/efficiency_percent.md @@ -0,0 +1,48 @@ + +# Slot: efficiency_percent + + +Percentage of volatile solids removed from the anaerobic digestor + +URI: [mixs.vocab:efficiency_percent](https://w3id.org/mixs/vocab/efficiency_percent) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | efficiency percent | +| **Mappings:** | | MIXS:0000657 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/elev.md b/mixs6/elev.md new file mode 100644 index 00000000..22a59058 --- /dev/null +++ b/mixs6/elev.md @@ -0,0 +1,238 @@ + +# Slot: elev + + +Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + +URI: [mixs.vocab:elev](https://w3id.org/mixs/vocab/elev) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | elevation | +| **Comments:** | | Expected value: measurement value | +| | | Position: 7.0 | +| | | This field is used in: 9 packages: air, host-associated, hydrocarbon resources-cores, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, water | +| **Examples:** | | Example(value='100 meter', description=None) | + diff --git a/mixs6/elevator.md b/mixs6/elevator.md new file mode 100644 index 00000000..3e825fd6 --- /dev/null +++ b/mixs6/elevator.md @@ -0,0 +1,47 @@ + +# Slot: elevator + + +The number of elevators within the built structure + +URI: [mixs.vocab:elevator](https://w3id.org/mixs/vocab/elevator) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | elevator count | +| **Mappings:** | | MIXS:0000799 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 63.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/emulsions.md b/mixs6/emulsions.md new file mode 100644 index 00000000..a00a23e4 --- /dev/null +++ b/mixs6/emulsions.md @@ -0,0 +1,48 @@ + +# Slot: emulsions + + +Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + +URI: [mixs.vocab:emulsions](https://w3id.org/mixs/vocab/emulsions) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | emulsions | +| **Mappings:** | | MIXS:0000660 | +| **Comments:** | | Expected value: emulsion name;measurement value | +| | | Preferred unit: gram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/encoded_traits.md b/mixs6/encoded_traits.md new file mode 100644 index 00000000..42523109 --- /dev/null +++ b/mixs6/encoded_traits.md @@ -0,0 +1,36 @@ + +# Slot: encoded_traits + + +Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + +URI: [mixs.vocab:encoded_traits](https://w3id.org/mixs/vocab/encoded_traits) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | encoded traits | +| **Comments:** | | Expected value: for plasmid: antibiotic resistance; for phage: converting genes | +| | | Position: 28.0 | +| **Examples:** | | Example(value='beta-lactamase class A', description=None) | + diff --git a/mixs6/env_broad_scale.md b/mixs6/env_broad_scale.md new file mode 100644 index 00000000..ebb63c03 --- /dev/null +++ b/mixs6/env_broad_scale.md @@ -0,0 +1,248 @@ + +# Slot: env_broad_scale + + +In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + +URI: [mixs.vocab:env_broad_scale](https://w3id.org/mixs/vocab/env_broad_scale) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + * [ME➞env_broad_scale](ME_env_broad_scale.md) + * [MIGS bacteria➞env_broad_scale](MIGS_bacteria_env_broad_scale.md) + * [MIGS eukaryote➞env_broad_scale](MIGS_eukaryote_env_broad_scale.md) + * [MIGS org➞env_broad_scale](MIGS_org_env_broad_scale.md) + * [MIGS plant➞env_broad_scale](MIGS_plant_env_broad_scale.md) + * [MIGS virus➞env_broad_scale](MIGS_virus_env_broad_scale.md) + * [MIMAG➞env_broad_scale](MIMAG_env_broad_scale.md) + * [MIMARKS specimen➞env_broad_scale](MIMARKS_specimen_env_broad_scale.md) + * [MIMARKS survey➞env_broad_scale](MIMARKS_survey_env_broad_scale.md) + * [MISAG➞env_broad_scale](MISAG_env_broad_scale.md) + * [MIUVIG➞env_broad_scale](MIUVIG_env_broad_scale.md) + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | broad-scale environmental context | +| **Comments:** | | Expected value: Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020] | +| | | Position: 10.0 | +| **Examples:** | | Example(value='forest biome [ENVO:01000174]', description=None) | + diff --git a/mixs6/env_local_scale.md b/mixs6/env_local_scale.md new file mode 100644 index 00000000..c824110b --- /dev/null +++ b/mixs6/env_local_scale.md @@ -0,0 +1,248 @@ + +# Slot: env_local_scale + + +In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + +URI: [mixs.vocab:env_local_scale](https://w3id.org/mixs/vocab/env_local_scale) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + * [ME➞env_local_scale](ME_env_local_scale.md) + * [MIGS bacteria➞env_local_scale](MIGS_bacteria_env_local_scale.md) + * [MIGS eukaryote➞env_local_scale](MIGS_eukaryote_env_local_scale.md) + * [MIGS org➞env_local_scale](MIGS_org_env_local_scale.md) + * [MIGS plant➞env_local_scale](MIGS_plant_env_local_scale.md) + * [MIGS virus➞env_local_scale](MIGS_virus_env_local_scale.md) + * [MIMAG➞env_local_scale](MIMAG_env_local_scale.md) + * [MIMARKS specimen➞env_local_scale](MIMARKS_specimen_env_local_scale.md) + * [MIMARKS survey➞env_local_scale](MIMARKS_survey_env_local_scale.md) + * [MISAG➞env_local_scale](MISAG_env_local_scale.md) + * [MIUVIG➞env_local_scale](MIUVIG_env_local_scale.md) + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | local environmental context | +| **Comments:** | | Expected value: Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316] | +| | | Position: 11.0 | +| **Examples:** | | Example(value='litter layer [ENVO:01000338]', description=None) | + diff --git a/mixs6/env_medium.md b/mixs6/env_medium.md new file mode 100644 index 00000000..35591c84 --- /dev/null +++ b/mixs6/env_medium.md @@ -0,0 +1,248 @@ + +# Slot: env_medium + + +In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + +URI: [mixs.vocab:env_medium](https://w3id.org/mixs/vocab/env_medium) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + * [ME➞env_medium](ME_env_medium.md) + * [MIGS bacteria➞env_medium](MIGS_bacteria_env_medium.md) + * [MIGS eukaryote➞env_medium](MIGS_eukaryote_env_medium.md) + * [MIGS org➞env_medium](MIGS_org_env_medium.md) + * [MIGS plant➞env_medium](MIGS_plant_env_medium.md) + * [MIGS virus➞env_medium](MIGS_virus_env_medium.md) + * [MIMAG➞env_medium](MIMAG_env_medium.md) + * [MIMARKS specimen➞env_medium](MIMARKS_specimen_env_medium.md) + * [MIMARKS survey➞env_medium](MIMARKS_survey_env_medium.md) + * [MISAG➞env_medium](MISAG_env_medium.md) + * [MIUVIG➞env_medium](MIUVIG_env_medium.md) + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | environmental medium | +| **Comments:** | | Expected value: Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160] | +| | | Position: 12.0 | +| **Examples:** | | Example(value='soil [ENVO:00001998]', description=None) | + diff --git a/mixs6/env_package.md b/mixs6/env_package.md new file mode 100644 index 00000000..872171ff --- /dev/null +++ b/mixs6/env_package.md @@ -0,0 +1,45 @@ + +# Slot: env_package + + +MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + +URI: [mixs.vocab:env_package](https://w3id.org/mixs/vocab/env_package) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [mixs extension field](mixs_extension_field.md) + +## Children + + * [ME➞env_package](ME_env_package.md) + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) + * [MIGS org➞env_package](MIGS_org_env_package.md) + * [MIGS plant➞env_package](MIGS_plant_env_package.md) + * [MIGS virus➞env_package](MIGS_virus_env_package.md) + * [MIMAG➞env_package](MIMAG_env_package.md) + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) + * [MISAG➞env_package](MISAG_env_package.md) + * [MIUVIG➞env_package](MIUVIG_env_package.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | environmental package | +| **Comments:** | | Expected value: enumeration | +| | | Position: 13.0 | +| **Examples:** | | Example(value='soil', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/64 | + diff --git a/mixs6/environment_field.md b/mixs6/environment_field.md new file mode 100644 index 00000000..f79c9ddd --- /dev/null +++ b/mixs6/environment_field.md @@ -0,0 +1,537 @@ + +# Slot: environment_field + + +field describing environmental aspect of a sample + +URI: [mixs.vocab:environment_field](https://w3id.org/mixs/vocab/environment_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [abs_air_humidity](abs_air_humidity.md) + * [add_recov_method](add_recov_method.md) + * [additional_info](additional_info.md) + * [address](address.md) + * [adj_room](adj_room.md) + * [aero_struc](aero_struc.md) + * [agrochem_addition](agrochem_addition.md) + * [air_temp](air_temp.md) + * [air_temp_regm](air_temp_regm.md) + * [al_sat](al_sat.md) + * [al_sat_meth](al_sat_meth.md) + * [alkalinity](alkalinity.md) + * [alkalinity_method](alkalinity_method.md) + * [alkyl_diethers](alkyl_diethers.md) + * [alt](alt.md) + * [aminopept_act](aminopept_act.md) + * [ammonium](ammonium.md) + * [amniotic_fluid_color](amniotic_fluid_color.md) + * [amount_light](amount_light.md) + * [ances_data](ances_data.md) + * [annual_precpt](annual_precpt.md) + * [annual_temp](annual_temp.md) + * [antibiotic_regm](antibiotic_regm.md) + * [api](api.md) + * [arch_struc](arch_struc.md) + * [aromatics_pc](aromatics_pc.md) + * [asphaltenes_pc](asphaltenes_pc.md) + * [atmospheric_data](atmospheric_data.md) + * [avg_dew_point](avg_dew_point.md) + * [avg_occup](avg_occup.md) + * [avg_temp](avg_temp.md) + * [bac_prod](bac_prod.md) + * [bac_resp](bac_resp.md) + * [bacteria_carb_prod](bacteria_carb_prod.md) + * [barometric_press](barometric_press.md) + * [basin](basin.md) + * [bathroom_count](bathroom_count.md) + * [bedroom_count](bedroom_count.md) + * [benzene](benzene.md) + * [biochem_oxygen_dem](biochem_oxygen_dem.md) + * [biocide](biocide.md) + * [biocide_admin_method](biocide_admin_method.md) + * [biol_stat](biol_stat.md) + * [biomass](biomass.md) + * [biotic_regm](biotic_regm.md) + * [birth_control](birth_control.md) + * [bishomohopanol](bishomohopanol.md) + * [blood_blood_disord](blood_blood_disord.md) + * [bromide](bromide.md) + * [build_docs](build_docs.md) + * [build_occup_type](build_occup_type.md) + * [building_setting](building_setting.md) + * [built_struc_age](built_struc_age.md) + * [built_struc_set](built_struc_set.md) + * [built_struc_type](built_struc_type.md) + * [calcium](calcium.md) + * [carb_dioxide](carb_dioxide.md) + * [carb_monoxide](carb_monoxide.md) + * [carb_nitro_ratio](carb_nitro_ratio.md) + * [ceil_area](ceil_area.md) + * [ceil_cond](ceil_cond.md) + * [ceil_finish_mat](ceil_finish_mat.md) + * [ceil_struc](ceil_struc.md) + * [ceil_texture](ceil_texture.md) + * [ceil_thermal_mass](ceil_thermal_mass.md) + * [ceil_type](ceil_type.md) + * [ceil_water_mold](ceil_water_mold.md) + * [chem_administration](chem_administration.md) + * [chem_mutagen](chem_mutagen.md) + * [chem_oxygen_dem](chem_oxygen_dem.md) + * [chem_treatment](chem_treatment.md) + * [chem_treatment_method](chem_treatment_method.md) + * [chloride](chloride.md) + * [chlorophyll](chlorophyll.md) + * [climate_environment](climate_environment.md) + * [collection_date](collection_date.md) + * [conduc](conduc.md) + * [cool_syst_id](cool_syst_id.md) + * [crop_rotation](crop_rotation.md) + * [cult_root_med](cult_root_med.md) + * [cur_land_use](cur_land_use.md) + * [cur_vegetation](cur_vegetation.md) + * [cur_vegetation_meth](cur_vegetation_meth.md) + * [date_last_rain](date_last_rain.md) + * [density](density.md) + * [depos_env](depos_env.md) + * [depth](depth.md) + * [dermatology_disord](dermatology_disord.md) + * [dew_point](dew_point.md) + * [diet_last_six_month](diet_last_six_month.md) + * [diether_lipids](diether_lipids.md) + * [diss_carb_dioxide](diss_carb_dioxide.md) + * [diss_hydrogen](diss_hydrogen.md) + * [diss_inorg_carb](diss_inorg_carb.md) + * [diss_inorg_nitro](diss_inorg_nitro.md) + * [diss_inorg_phosp](diss_inorg_phosp.md) + * [diss_iron](diss_iron.md) + * [diss_org_carb](diss_org_carb.md) + * [diss_org_nitro](diss_org_nitro.md) + * [diss_oxygen](diss_oxygen.md) + * [diss_oxygen_fluid](diss_oxygen_fluid.md) + * [dominant_hand](dominant_hand.md) + * [door_comp_type](door_comp_type.md) + * [door_cond](door_cond.md) + * [door_direct](door_direct.md) + * [door_loc](door_loc.md) + * [door_mat](door_mat.md) + * [door_move](door_move.md) + * [door_size](door_size.md) + * [door_type](door_type.md) + * [door_type_metal](door_type_metal.md) + * [door_type_wood](door_type_wood.md) + * [door_water_mold](door_water_mold.md) + * [douche](douche.md) + * [down_par](down_par.md) + * [drainage_class](drainage_class.md) + * [drawings](drawings.md) + * [drug_usage](drug_usage.md) + * [efficiency_percent](efficiency_percent.md) + * [elev](elev.md) + * [elevator](elevator.md) + * [emulsions](emulsions.md) + * [env_broad_scale](env_broad_scale.md) + * [env_local_scale](env_local_scale.md) + * [env_medium](env_medium.md) + * [escalator](escalator.md) + * [ethylbenzene](ethylbenzene.md) + * [exp_duct](exp_duct.md) + * [exp_pipe](exp_pipe.md) + * [ext_door](ext_door.md) + * [ext_wall_orient](ext_wall_orient.md) + * [ext_window_orient](ext_window_orient.md) + * [extreme_event](extreme_event.md) + * [extreme_salinity](extreme_salinity.md) + * [fao_class](fao_class.md) + * [fertilizer_regm](fertilizer_regm.md) + * [field](field.md) + * [filter_type](filter_type.md) + * [fire](fire.md) + * [fireplace_type](fireplace_type.md) + * [flooding](flooding.md) + * [floor_age](floor_age.md) + * [floor_area](floor_area.md) + * [floor_cond](floor_cond.md) + * [floor_count](floor_count.md) + * [floor_finish_mat](floor_finish_mat.md) + * [floor_struc](floor_struc.md) + * [floor_thermal_mass](floor_thermal_mass.md) + * [floor_water_mold](floor_water_mold.md) + * [fluor](fluor.md) + * [foetal_health_stat](foetal_health_stat.md) + * [freq_clean](freq_clean.md) + * [freq_cook](freq_cook.md) + * [fungicide_regm](fungicide_regm.md) + * [furniture](furniture.md) + * [gaseous_environment](gaseous_environment.md) + * [gaseous_substances](gaseous_substances.md) + * [gastrointest_disord](gastrointest_disord.md) + * [gender_restroom](gender_restroom.md) + * [genetic_mod](genetic_mod.md) + * [geo_loc_name](geo_loc_name.md) + * [gestation_state](gestation_state.md) + * [glucosidase_act](glucosidase_act.md) + * [gravidity](gravidity.md) + * [gravity](gravity.md) + * [growth_facil](growth_facil.md) + * [growth_habit](growth_habit.md) + * [growth_hormone_regm](growth_hormone_regm.md) + * [gynecologic_disord](gynecologic_disord.md) + * [hall_count](hall_count.md) + * [handidness](handidness.md) + * [hc_produced](hc_produced.md) + * [hcr](hcr.md) + * [hcr_fw_salinity](hcr_fw_salinity.md) + * [hcr_geol_age](hcr_geol_age.md) + * [hcr_pressure](hcr_pressure.md) + * [hcr_temp](hcr_temp.md) + * [heat_cool_type](heat_cool_type.md) + * [heat_deliv_loc](heat_deliv_loc.md) + * [heat_system_deliv_meth](heat_system_deliv_meth.md) + * [heat_system_id](heat_system_id.md) + * [heavy_metals](heavy_metals.md) + * [heavy_metals_meth](heavy_metals_meth.md) + * [height_carper_fiber](height_carper_fiber.md) + * [herbicide_regm](herbicide_regm.md) + * [horizon](horizon.md) + * [horizon_meth](horizon_meth.md) + * [host_age](host_age.md) + * [host_blood_press_diast](host_blood_press_diast.md) + * [host_blood_press_syst](host_blood_press_syst.md) + * [host_body_habitat](host_body_habitat.md) + * [host_body_mass_index](host_body_mass_index.md) + * [host_body_product](host_body_product.md) + * [host_body_site](host_body_site.md) + * [host_body_temp](host_body_temp.md) + * [host_color](host_color.md) + * [host_common_name](host_common_name.md) + * [host_diet](host_diet.md) + * [host_disease_stat](host_disease_stat.md) + * [host_dry_mass](host_dry_mass.md) + * [host_family_relationship](host_family_relationship.md) + * [host_genotype](host_genotype.md) + * [host_growth_cond](host_growth_cond.md) + * [host_height](host_height.md) + * [host_hiv_stat](host_hiv_stat.md) + * [host_infra_specific_name](host_infra_specific_name.md) + * [host_infra_specific_rank](host_infra_specific_rank.md) + * [host_last_meal](host_last_meal.md) + * [host_length](host_length.md) + * [host_life_stage](host_life_stage.md) + * [host_occupation](host_occupation.md) + * [host_phenotype](host_phenotype.md) + * [host_pulse](host_pulse.md) + * [host_sex](host_sex.md) + * [host_shape](host_shape.md) + * [host_subject_id](host_subject_id.md) + * [host_substrate](host_substrate.md) + * [host_symbiont](host_symbiont.md) + * [host_taxid](host_taxid.md) + * [host_tot_mass](host_tot_mass.md) + * [host_wet_mass](host_wet_mass.md) + * [hrt](hrt.md) + * [humidity](humidity.md) + * [humidity_regm](humidity_regm.md) + * [hysterectomy](hysterectomy.md) + * [ihmc_ethnicity](ihmc_ethnicity.md) + * [ihmc_medication_code](ihmc_medication_code.md) + * [indoor_space](indoor_space.md) + * [indoor_surf](indoor_surf.md) + * [indust_eff_percent](indust_eff_percent.md) + * [inorg_particles](inorg_particles.md) + * [inside_lux](inside_lux.md) + * [int_wall_cond](int_wall_cond.md) + * [iw_bt_date_well](iw_bt_date_well.md) + * [iwf](iwf.md) + * [kidney_disord](kidney_disord.md) + * [last_clean](last_clean.md) + * [lat_lon](lat_lon.md) + * [light_intensity](light_intensity.md) + * [light_regm](light_regm.md) + * [light_type](light_type.md) + * [link_addit_analys](link_addit_analys.md) + * [link_class_info](link_class_info.md) + * [link_climate_info](link_climate_info.md) + * [lithology](lithology.md) + * [liver_disord](liver_disord.md) + * [local_class](local_class.md) + * [local_class_meth](local_class_meth.md) + * [magnesium](magnesium.md) + * [maternal_health_stat](maternal_health_stat.md) + * [max_occup](max_occup.md) + * [mean_frict_vel](mean_frict_vel.md) + * [mean_peak_frict_vel](mean_peak_frict_vel.md) + * [mech_struc](mech_struc.md) + * [mechanical_damage](mechanical_damage.md) + * [medic_hist_perform](medic_hist_perform.md) + * [menarche](menarche.md) + * [menopause](menopause.md) + * [methane](methane.md) + * [microbial_biomass](microbial_biomass.md) + * [microbial_biomass_meth](microbial_biomass_meth.md) + * [mineral_nutr_regm](mineral_nutr_regm.md) + * [misc_param](misc_param.md) + * [n_alkanes](n_alkanes.md) + * [nitrate](nitrate.md) + * [nitrite](nitrite.md) + * [nitro](nitro.md) + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) + * [nose_throat_disord](nose_throat_disord.md) + * [number_pets](number_pets.md) + * [number_plants](number_plants.md) + * [number_resident](number_resident.md) + * [occup_density_samp](occup_density_samp.md) + * [occup_document](occup_document.md) + * [occup_samp](occup_samp.md) + * [org_carb](org_carb.md) + * [org_matter](org_matter.md) + * [org_nitro](org_nitro.md) + * [org_particles](org_particles.md) + * [organism_count](organism_count.md) + * [organism_count_qpcr_info](organism_count_qpcr_info.md) + * [owc_tvdss](owc_tvdss.md) + * [oxy_stat_samp](oxy_stat_samp.md) + * [oxygen](oxygen.md) + * [part_org_carb](part_org_carb.md) + * [part_org_nitro](part_org_nitro.md) + * [particle_class](particle_class.md) + * [permeability](permeability.md) + * [perturbation](perturbation.md) + * [pesticide_regm](pesticide_regm.md) + * [pet_farm_animal](pet_farm_animal.md) + * [petroleum_hydrocarb](petroleum_hydrocarb.md) + * [ph](ph.md) + * [ph_meth](ph_meth.md) + * [ph_regm](ph_regm.md) + * [phaeopigments](phaeopigments.md) + * [phosphate](phosphate.md) + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) + * [photon_flux](photon_flux.md) + * [plant_growth_med](plant_growth_med.md) + * [plant_product](plant_product.md) + * [plant_sex](plant_sex.md) + * [plant_struc](plant_struc.md) + * [pollutants](pollutants.md) + * [pool_dna_extracts](pool_dna_extracts.md) + * [porosity](porosity.md) + * [potassium](potassium.md) + * [pour_point](pour_point.md) + * [pre_treatment](pre_treatment.md) + * [pregnancy](pregnancy.md) + * [pres_animal](pres_animal.md) + * [pressure](pressure.md) + * [previous_land_use](previous_land_use.md) + * [previous_land_use_meth](previous_land_use_meth.md) + * [primary_prod](primary_prod.md) + * [primary_treatment](primary_treatment.md) + * [prod_rate](prod_rate.md) + * [prod_start_date](prod_start_date.md) + * [profile_position](profile_position.md) + * [pulmonary_disord](pulmonary_disord.md) + * [quad_pos](quad_pos.md) + * [radiation_regm](radiation_regm.md) + * [rainfall_regm](rainfall_regm.md) + * [reactor_type](reactor_type.md) + * [redox_potential](redox_potential.md) + * [rel_air_humidity](rel_air_humidity.md) + * [rel_humidity_out](rel_humidity_out.md) + * [rel_samp_loc](rel_samp_loc.md) + * [reservoir](reservoir.md) + * [resins_pc](resins_pc.md) + * [resp_part_matter](resp_part_matter.md) + * [room_air_exch_rate](room_air_exch_rate.md) + * [room_architec_element](room_architec_element.md) + * [room_condt](room_condt.md) + * [room_connected](room_connected.md) + * [room_count](room_count.md) + * [room_dim](room_dim.md) + * [room_door_dist](room_door_dist.md) + * [room_door_share](room_door_share.md) + * [room_hallway](room_hallway.md) + * [room_loc](room_loc.md) + * [room_moist_damage_hist](room_moist_damage_hist.md) + * [room_net_area](room_net_area.md) + * [room_occup](room_occup.md) + * [room_samp_pos](room_samp_pos.md) + * [room_type](room_type.md) + * [room_vol](room_vol.md) + * [room_wall_share](room_wall_share.md) + * [room_window_count](room_window_count.md) + * [root_cond](root_cond.md) + * [root_med_carbon](root_med_carbon.md) + * [root_med_macronutr](root_med_macronutr.md) + * [root_med_micronutr](root_med_micronutr.md) + * [root_med_ph](root_med_ph.md) + * [root_med_regl](root_med_regl.md) + * [root_med_solid](root_med_solid.md) + * [root_med_suppl](root_med_suppl.md) + * [salinity](salinity.md) + * [salinity_meth](salinity_meth.md) + * [salt_regm](salt_regm.md) + * [samp_capt_status](samp_capt_status.md) + * [samp_collection_point](samp_collection_point.md) + * [samp_dis_stage](samp_dis_stage.md) + * [samp_floor](samp_floor.md) + * [samp_loc_corr_rate](samp_loc_corr_rate.md) + * [samp_md](samp_md.md) + * [samp_preserv](samp_preserv.md) + * [samp_room_id](samp_room_id.md) + * [samp_salinity](samp_salinity.md) + * [samp_sort_meth](samp_sort_meth.md) + * [samp_store_dur](samp_store_dur.md) + * [samp_store_loc](samp_store_loc.md) + * [samp_store_temp](samp_store_temp.md) + * [samp_subtype](samp_subtype.md) + * [samp_time_out](samp_time_out.md) + * [samp_transport_cond](samp_transport_cond.md) + * [samp_tvdss](samp_tvdss.md) + * [samp_type](samp_type.md) + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) + * [samp_weather](samp_weather.md) + * [samp_well_name](samp_well_name.md) + * [saturates_pc](saturates_pc.md) + * [season](season.md) + * [season_environment](season_environment.md) + * [season_precpt](season_precpt.md) + * [season_temp](season_temp.md) + * [season_use](season_use.md) + * [secondary_treatment](secondary_treatment.md) + * [sediment_type](sediment_type.md) + * [sewage_type](sewage_type.md) + * [sexual_act](sexual_act.md) + * [shading_device_cond](shading_device_cond.md) + * [shading_device_loc](shading_device_loc.md) + * [shading_device_mat](shading_device_mat.md) + * [shading_device_type](shading_device_type.md) + * [shading_device_water_mold](shading_device_water_mold.md) + * [sieving](sieving.md) + * [silicate](silicate.md) + * [size_frac_low](size_frac_low.md) + * [size_frac_up](size_frac_up.md) + * [slope_aspect](slope_aspect.md) + * [slope_gradient](slope_gradient.md) + * [sludge_retent_time](sludge_retent_time.md) + * [smoker](smoker.md) + * [sodium](sodium.md) + * [soil_type](soil_type.md) + * [soil_type_meth](soil_type_meth.md) + * [solar_irradiance](solar_irradiance.md) + * [soluble_inorg_mat](soluble_inorg_mat.md) + * [soluble_org_mat](soluble_org_mat.md) + * [soluble_react_phosp](soluble_react_phosp.md) + * [space_typ_state](space_typ_state.md) + * [special_diet](special_diet.md) + * [specific](specific.md) + * [specific_humidity](specific_humidity.md) + * [sr_dep_env](sr_dep_env.md) + * [sr_geol_age](sr_geol_age.md) + * [sr_kerog_type](sr_kerog_type.md) + * [sr_lithology](sr_lithology.md) + * [standing_water_regm](standing_water_regm.md) + * [store_cond](store_cond.md) + * [study_complt_stat](study_complt_stat.md) + * [substructure_type](substructure_type.md) + * [sulfate](sulfate.md) + * [sulfate_fw](sulfate_fw.md) + * [sulfide](sulfide.md) + * [surf_air_cont](surf_air_cont.md) + * [surf_humidity](surf_humidity.md) + * [surf_material](surf_material.md) + * [surf_moisture](surf_moisture.md) + * [surf_moisture_ph](surf_moisture_ph.md) + * [surf_temp](surf_temp.md) + * [suspend_part_matter](suspend_part_matter.md) + * [suspend_solids](suspend_solids.md) + * [tan](tan.md) + * [temp](temp.md) + * [temp_out](temp_out.md) + * [tertiary_treatment](tertiary_treatment.md) + * [texture](texture.md) + * [texture_meth](texture_meth.md) + * [tidal_stage](tidal_stage.md) + * [tillage](tillage.md) + * [time_last_toothbrush](time_last_toothbrush.md) + * [time_since_last_wash](time_since_last_wash.md) + * [tiss_cult_growth_med](tiss_cult_growth_med.md) + * [toluene](toluene.md) + * [tot_carb](tot_carb.md) + * [tot_depth_water_col](tot_depth_water_col.md) + * [tot_diss_nitro](tot_diss_nitro.md) + * [tot_inorg_nitro](tot_inorg_nitro.md) + * [tot_iron](tot_iron.md) + * [tot_nitro](tot_nitro.md) + * [tot_nitro_content](tot_nitro_content.md) + * [tot_nitro_content_meth](tot_nitro_content_meth.md) + * [tot_org_c_meth](tot_org_c_meth.md) + * [tot_org_carb](tot_org_carb.md) + * [tot_part_carb](tot_part_carb.md) + * [tot_phosp](tot_phosp.md) + * [tot_phosphate](tot_phosphate.md) + * [tot_sulfur](tot_sulfur.md) + * [train_line](train_line.md) + * [train_stat_loc](train_stat_loc.md) + * [train_stop_loc](train_stop_loc.md) + * [travel_out_six_month](travel_out_six_month.md) + * [turbidity](turbidity.md) + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) + * [twin_sibling](twin_sibling.md) + * [typ_occup_density](typ_occup_density.md) + * [urine_collect_meth](urine_collect_meth.md) + * [urogenit_disord](urogenit_disord.md) + * [urogenit_tract_disor](urogenit_tract_disor.md) + * [ventilation_rate](ventilation_rate.md) + * [ventilation_type](ventilation_type.md) + * [vfa](vfa.md) + * [vfa_fw](vfa_fw.md) + * [vis_media](vis_media.md) + * [viscosity](viscosity.md) + * [volatile_org_comp](volatile_org_comp.md) + * [wall_area](wall_area.md) + * [wall_const_type](wall_const_type.md) + * [wall_finish_mat](wall_finish_mat.md) + * [wall_height](wall_height.md) + * [wall_loc](wall_loc.md) + * [wall_surf_treatment](wall_surf_treatment.md) + * [wall_texture](wall_texture.md) + * [wall_thermal_mass](wall_thermal_mass.md) + * [wall_water_mold](wall_water_mold.md) + * [wastewater_type](wastewater_type.md) + * [water_content](water_content.md) + * [water_content_soil_meth](water_content_soil_meth.md) + * [water_current](water_current.md) + * [water_cut](water_cut.md) + * [water_feat_size](water_feat_size.md) + * [water_feat_type](water_feat_type.md) + * [water_production_rate](water_production_rate.md) + * [water_temp_regm](water_temp_regm.md) + * [watering_regm](watering_regm.md) + * [weekday](weekday.md) + * [weight_loss_3_month](weight_loss_3_month.md) + * [win](win.md) + * [wind_direction](wind_direction.md) + * [wind_speed](wind_speed.md) + * [window_cond](window_cond.md) + * [window_cover](window_cover.md) + * [window_horiz_pos](window_horiz_pos.md) + * [window_loc](window_loc.md) + * [window_mat](window_mat.md) + * [window_open_freq](window_open_freq.md) + * [window_size](window_size.md) + * [window_status](window_status.md) + * [window_type](window_type.md) + * [window_vert_pos](window_vert_pos.md) + * [window_water_mold](window_water_mold.md) + * [xylene](xylene.md) + +## Used by + diff --git a/mixs6/escalator.md b/mixs6/escalator.md new file mode 100644 index 00000000..f819dd25 --- /dev/null +++ b/mixs6/escalator.md @@ -0,0 +1,47 @@ + +# Slot: escalator + + +The number of escalators within the built structure + +URI: [mixs.vocab:escalator](https://w3id.org/mixs/vocab/escalator) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | escalator count | +| **Mappings:** | | MIXS:0000800 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 64.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='4', description=None) | + diff --git a/mixs6/estimated_size.md b/mixs6/estimated_size.md new file mode 100644 index 00000000..d92bddec --- /dev/null +++ b/mixs6/estimated_size.md @@ -0,0 +1,39 @@ + +# Slot: estimated_size + + +The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + +URI: [mixs.vocab:estimated_size](https://w3id.org/mixs/vocab/estimated_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | estimated size | +| **Comments:** | | Expected value: number of base pairs | +| | | Position: 18.0 | +| **Examples:** | | Example(value='300000 bp', description=None) | + diff --git a/mixs6/ethylbenzene.md b/mixs6/ethylbenzene.md new file mode 100644 index 00000000..49ceb99e --- /dev/null +++ b/mixs6/ethylbenzene.md @@ -0,0 +1,60 @@ + +# Slot: ethylbenzene + + +Concentration of ethylbenzene in the sample + +URI: [mixs.vocab:ethylbenzene](https://w3id.org/mixs/vocab/ethylbenzene) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ethylbenzene | +| **Mappings:** | | MIXS:0000155 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 83.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/exp_duct.md b/mixs6/exp_duct.md new file mode 100644 index 00000000..19d1f2be --- /dev/null +++ b/mixs6/exp_duct.md @@ -0,0 +1,48 @@ + +# Slot: exp_duct + + +The amount of exposed ductwork in the room + +URI: [mixs.vocab:exp_duct](https://w3id.org/mixs/vocab/exp_duct) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | exposed ductwork | +| **Mappings:** | | MIXS:0000144 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 65.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/exp_pipe.md b/mixs6/exp_pipe.md new file mode 100644 index 00000000..572707ee --- /dev/null +++ b/mixs6/exp_pipe.md @@ -0,0 +1,47 @@ + +# Slot: exp_pipe + + +The number of exposed pipes in the room + +URI: [mixs.vocab:exp_pipe](https://w3id.org/mixs/vocab/exp_pipe) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | exposed pipes | +| **Mappings:** | | MIXS:0000220 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 66.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/experimental_factor.md b/mixs6/experimental_factor.md new file mode 100644 index 00000000..62063901 --- /dev/null +++ b/mixs6/experimental_factor.md @@ -0,0 +1,44 @@ + +# Slot: experimental_factor + + +Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + +URI: [mixs.vocab:experimental_factor](https://w3id.org/mixs/vocab/experimental_factor) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + * [ME➞experimental_factor](ME_experimental_factor.md) + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | experimental factor | +| **Comments:** | | Expected value: text or EFO and/or OBI | +| | | Position: 4.0 | +| **Examples:** | | Example(value='time series design [EFO:EFO_0001779]', description=None) | + diff --git a/mixs6/ext_door.md b/mixs6/ext_door.md new file mode 100644 index 00000000..474e604a --- /dev/null +++ b/mixs6/ext_door.md @@ -0,0 +1,47 @@ + +# Slot: ext_door + + +The number of exterior doors in the built structure + +URI: [mixs.vocab:ext_door](https://w3id.org/mixs/vocab/ext_door) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | exterior door count | +| **Mappings:** | | MIXS:0000170 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 67.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ext_wall_orient.md b/mixs6/ext_wall_orient.md new file mode 100644 index 00000000..cbebcd19 --- /dev/null +++ b/mixs6/ext_wall_orient.md @@ -0,0 +1,47 @@ + +# Slot: ext_wall_orient + + +The orientation of the exterior wall + +URI: [mixs.vocab:ext_wall_orient](https://w3id.org/mixs/vocab/ext_wall_orient) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | orientations of exterior wall | +| **Mappings:** | | MIXS:0000817 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 96.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='northwest', description=None) | + diff --git a/mixs6/ext_window_orient.md b/mixs6/ext_window_orient.md new file mode 100644 index 00000000..f1899156 --- /dev/null +++ b/mixs6/ext_window_orient.md @@ -0,0 +1,47 @@ + +# Slot: ext_window_orient + + +The compass direction the exterior window of the room is facing + +URI: [mixs.vocab:ext_window_orient](https://w3id.org/mixs/vocab/ext_window_orient) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | orientations of exterior window | +| **Mappings:** | | MIXS:0000818 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 97.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='southwest', description=None) | + diff --git a/mixs6/extrachrom_elements.md b/mixs6/extrachrom_elements.md new file mode 100644 index 00000000..65d97c26 --- /dev/null +++ b/mixs6/extrachrom_elements.md @@ -0,0 +1,37 @@ + +# Slot: extrachrom_elements + + +Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + +URI: [mixs.vocab:extrachrom_elements](https://w3id.org/mixs/vocab/extrachrom_elements) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extrachromosomal elements | +| **Comments:** | | Expected value: number of extrachromosmal elements | +| | | Position: 17.0 | +| **Examples:** | | Example(value='5', description=None) | + diff --git a/mixs6/extreme_event.md b/mixs6/extreme_event.md new file mode 100644 index 00000000..f92b79b2 --- /dev/null +++ b/mixs6/extreme_event.md @@ -0,0 +1,47 @@ + +# Slot: extreme_event + + +Unusual physical events that may have affected microbial populations + +URI: [mixs.vocab:extreme_event](https://w3id.org/mixs/vocab/extreme_event) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/extreme events | +| **Mappings:** | | MIXS:0000320 | +| **Comments:** | | Expected value: date | +| | | Occurrence: 1 | +| | | Position: 11.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/extreme_salinity.md b/mixs6/extreme_salinity.md new file mode 100644 index 00000000..2a20916d --- /dev/null +++ b/mixs6/extreme_salinity.md @@ -0,0 +1,48 @@ + +# Slot: extreme_salinity + + +Measured salinity + +URI: [mixs.vocab:extreme_salinity](https://w3id.org/mixs/vocab/extreme_salinity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/salinity | +| **Mappings:** | | MIXS:0000651 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millisiemens per meter | +| | | Occurrence: 1 | +| | | Position: 46.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/fao_class.md b/mixs6/fao_class.md new file mode 100644 index 00000000..38b6aff2 --- /dev/null +++ b/mixs6/fao_class.md @@ -0,0 +1,47 @@ + +# Slot: fao_class + + +Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + +URI: [mixs.vocab:fao_class](https://w3id.org/mixs/vocab/fao_class) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil_taxonomic/FAO classification | +| **Mappings:** | | MIXS:0001083 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 26.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='Luvisols', description=None) | + diff --git a/mixs6/feat_pred.md b/mixs6/feat_pred.md new file mode 100644 index 00000000..2f98731e --- /dev/null +++ b/mixs6/feat_pred.md @@ -0,0 +1,42 @@ + +# Slot: feat_pred + + +Method used to predict UViGs features such as ORFs, integration site, etc. + +URI: [mixs.vocab:feat_pred](https://w3id.org/mixs/vocab/feat_pred) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞feat_pred](ME_feat_pred.md) + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) + * [MISAG➞feat_pred](MISAG_feat_pred.md) + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | feature prediction | +| **Comments:** | | Expected value: names and versions of software(s), parameters used | +| | | Position: 59.0 | +| **Examples:** | | Example(value='Prodigal;2.6.3;default parameters', description=None) | + diff --git a/mixs6/fertilizer_regm.md b/mixs6/fertilizer_regm.md new file mode 100644 index 00000000..01020148 --- /dev/null +++ b/mixs6/fertilizer_regm.md @@ -0,0 +1,48 @@ + +# Slot: fertilizer_regm + + +Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + +URI: [mixs.vocab:fertilizer_regm](https://w3id.org/mixs/vocab/fertilizer_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fertilizer regimen | +| **Mappings:** | | MIXS:0000556 | +| **Comments:** | | Expected value: fertilizer name;fertilizer amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/field.md b/mixs6/field.md new file mode 100644 index 00000000..9e36c2e0 --- /dev/null +++ b/mixs6/field.md @@ -0,0 +1,59 @@ + +# Slot: field + + +Name of the hydrocarbon field (e.g. Albacora) + +URI: [mixs.vocab:field](https://w3id.org/mixs/vocab/field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | field name | +| **Mappings:** | | MIXS:0000291 | +| **Comments:** | | Expected value: name | +| | | Occurrence: 1 | +| | | Position: 4.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/filter_type.md b/mixs6/filter_type.md new file mode 100644 index 00000000..f10e1221 --- /dev/null +++ b/mixs6/filter_type.md @@ -0,0 +1,47 @@ + +# Slot: filter_type + + +A device which removes solid particulates or airborne molecular contaminants + +URI: [mixs.vocab:filter_type](https://w3id.org/mixs/vocab/filter_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | filter type | +| **Mappings:** | | MIXS:0000765 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 17.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='HEPA', description=None) | + diff --git a/mixs6/fire.md b/mixs6/fire.md new file mode 100644 index 00000000..1aefb8dd --- /dev/null +++ b/mixs6/fire.md @@ -0,0 +1,47 @@ + +# Slot: fire + + +Historical and/or physical evidence of fire + +URI: [mixs.vocab:fire](https://w3id.org/mixs/vocab/fire) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/fire | +| **Mappings:** | | MIXS:0001086 | +| **Comments:** | | Expected value: date | +| | | Occurrence: 1 | +| | | Position: 9.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/fireplace_type.md b/mixs6/fireplace_type.md new file mode 100644 index 00000000..d1c3f382 --- /dev/null +++ b/mixs6/fireplace_type.md @@ -0,0 +1,47 @@ + +# Slot: fireplace_type + + +A firebox with chimney + +URI: [mixs.vocab:fireplace_type](https://w3id.org/mixs/vocab/fireplace_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fireplace type | +| **Mappings:** | | MIXS:0000802 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 68.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood burning', description=None) | + diff --git a/mixs6/flooding.md b/mixs6/flooding.md new file mode 100644 index 00000000..ec726bc5 --- /dev/null +++ b/mixs6/flooding.md @@ -0,0 +1,47 @@ + +# Slot: flooding + + +Historical and/or physical evidence of flooding + +URI: [mixs.vocab:flooding](https://w3id.org/mixs/vocab/flooding) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/flooding | +| **Mappings:** | | MIXS:0000319 | +| **Comments:** | | Expected value: date | +| | | Occurrence: 1 | +| | | Position: 10.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_age.md b/mixs6/floor_age.md new file mode 100644 index 00000000..6b90b689 --- /dev/null +++ b/mixs6/floor_age.md @@ -0,0 +1,48 @@ + +# Slot: floor_age + + +The time period since installment of the carpet or flooring + +URI: [mixs.vocab:floor_age](https://w3id.org/mixs/vocab/floor_age) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor age | +| **Mappings:** | | MIXS:0000164 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: years, weeks, days | +| | | Occurrence: 1 | +| | | Position: 69.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_area.md b/mixs6/floor_area.md new file mode 100644 index 00000000..d178fb55 --- /dev/null +++ b/mixs6/floor_area.md @@ -0,0 +1,48 @@ + +# Slot: floor_area + + +The area of the floor space within the room + +URI: [mixs.vocab:floor_area](https://w3id.org/mixs/vocab/floor_area) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor area | +| **Mappings:** | | MIXS:0000165 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 70.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_cond.md b/mixs6/floor_cond.md new file mode 100644 index 00000000..3fb6ff53 --- /dev/null +++ b/mixs6/floor_cond.md @@ -0,0 +1,47 @@ + +# Slot: floor_cond + + +The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + +URI: [mixs.vocab:floor_cond](https://w3id.org/mixs/vocab/floor_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor condition | +| **Mappings:** | | MIXS:0000803 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 71.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/floor_count.md b/mixs6/floor_count.md new file mode 100644 index 00000000..b021aa11 --- /dev/null +++ b/mixs6/floor_count.md @@ -0,0 +1,47 @@ + +# Slot: floor_count + + +The number of floors in the building, including basements and mechanical penthouse + +URI: [mixs.vocab:floor_count](https://w3id.org/mixs/vocab/floor_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor count | +| **Mappings:** | | MIXS:0000225 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 72.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_finish_mat.md b/mixs6/floor_finish_mat.md new file mode 100644 index 00000000..68217df8 --- /dev/null +++ b/mixs6/floor_finish_mat.md @@ -0,0 +1,47 @@ + +# Slot: floor_finish_mat + + +The floor covering type; the finished surface that is walked on + +URI: [mixs.vocab:floor_finish_mat](https://w3id.org/mixs/vocab/floor_finish_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor finish material | +| **Mappings:** | | MIXS:0000804 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 73.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='carpet', description=None) | + diff --git a/mixs6/floor_struc.md b/mixs6/floor_struc.md new file mode 100644 index 00000000..4e2a340b --- /dev/null +++ b/mixs6/floor_struc.md @@ -0,0 +1,47 @@ + +# Slot: floor_struc + + +Refers to the structural elements and subfloor upon which the finish flooring is installed + +URI: [mixs.vocab:floor_struc](https://w3id.org/mixs/vocab/floor_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor structure | +| **Mappings:** | | MIXS:0000806 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 75.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='concrete', description=None) | + diff --git a/mixs6/floor_thermal_mass.md b/mixs6/floor_thermal_mass.md new file mode 100644 index 00000000..c5173ccc --- /dev/null +++ b/mixs6/floor_thermal_mass.md @@ -0,0 +1,48 @@ + +# Slot: floor_thermal_mass + + +The ability of the floor to provide inertia against temperature fluctuations + +URI: [mixs.vocab:floor_thermal_mass](https://w3id.org/mixs/vocab/floor_thermal_mass) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor thermal mass | +| **Mappings:** | | MIXS:0000166 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: joule per degree Celsius | +| | | Occurrence: 1 | +| | | Position: 76.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_water_mold.md b/mixs6/floor_water_mold.md new file mode 100644 index 00000000..307f8a35 --- /dev/null +++ b/mixs6/floor_water_mold.md @@ -0,0 +1,47 @@ + +# Slot: floor_water_mold + + +Signs of the presence of mold or mildew in a room + +URI: [mixs.vocab:floor_water_mold](https://w3id.org/mixs/vocab/floor_water_mold) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor signs of water/mold | +| **Mappings:** | | MIXS:0000805 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 74.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='ceiling discoloration', description=None) | + diff --git a/mixs6/fluor.md b/mixs6/fluor.md new file mode 100644 index 00000000..2a3bc554 --- /dev/null +++ b/mixs6/fluor.md @@ -0,0 +1,48 @@ + +# Slot: fluor + + +Raw or converted fluorescence of water + +URI: [mixs.vocab:fluor](https://w3id.org/mixs/vocab/fluor) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fluorescence | +| **Mappings:** | | MIXS:0000704 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram chlorophyll a per cubic meter, volts | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='2.5 volts', description=None) | + diff --git a/mixs6/foetal_health_stat.md b/mixs6/foetal_health_stat.md new file mode 100644 index 00000000..3ddbd1a6 --- /dev/null +++ b/mixs6/foetal_health_stat.md @@ -0,0 +1,47 @@ + +# Slot: foetal_health_stat + + +Specification of foetal health status, should also include abortion + +URI: [mixs.vocab:foetal_health_stat](https://w3id.org/mixs/vocab/foetal_health_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/foetal health status | +| **Mappings:** | | MIXS:0000275 | +| **Comments:** | | Expected value: health status | +| | | Occurrence: 1 | +| | | Position: 38.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/freq_clean.md b/mixs6/freq_clean.md new file mode 100644 index 00000000..71c28f02 --- /dev/null +++ b/mixs6/freq_clean.md @@ -0,0 +1,47 @@ + +# Slot: freq_clean + + +The number of times the building is cleaned per week + +URI: [mixs.vocab:freq_clean](https://w3id.org/mixs/vocab/freq_clean) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | frequency of cleaning | +| **Mappings:** | | MIXS:0000226 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 77.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/freq_cook.md b/mixs6/freq_cook.md new file mode 100644 index 00000000..e6e6c3d3 --- /dev/null +++ b/mixs6/freq_cook.md @@ -0,0 +1,47 @@ + +# Slot: freq_cook + + +The number of times a meal is cooked per week + +URI: [mixs.vocab:freq_cook](https://w3id.org/mixs/vocab/freq_cook) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | frequency of cooking | +| **Mappings:** | | MIXS:0000227 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 78.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/fungicide_regm.md b/mixs6/fungicide_regm.md new file mode 100644 index 00000000..38239a56 --- /dev/null +++ b/mixs6/fungicide_regm.md @@ -0,0 +1,48 @@ + +# Slot: fungicide_regm + + +Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + +URI: [mixs.vocab:fungicide_regm](https://w3id.org/mixs/vocab/fungicide_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fungicide regimen | +| **Mappings:** | | MIXS:0000557 | +| **Comments:** | | Expected value: fungicide name;fungicide amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/furniture.md b/mixs6/furniture.md new file mode 100644 index 00000000..22cfaf78 --- /dev/null +++ b/mixs6/furniture.md @@ -0,0 +1,47 @@ + +# Slot: furniture + + +The types of furniture present in the sampled room + +URI: [mixs.vocab:furniture](https://w3id.org/mixs/vocab/furniture) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | furniture | +| **Mappings:** | | MIXS:0000807 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 79.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='chair', description=None) | + diff --git a/mixs6/gaseous_environment.md b/mixs6/gaseous_environment.md new file mode 100644 index 00000000..afbe5c82 --- /dev/null +++ b/mixs6/gaseous_environment.md @@ -0,0 +1,48 @@ + +# Slot: gaseous_environment + + +Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + +URI: [mixs.vocab:gaseous_environment](https://w3id.org/mixs/vocab/gaseous_environment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gaseous environment | +| **Mappings:** | | MIXS:0000558 | +| **Comments:** | | Expected value: gaseous compound name;gaseous compound amount;treatment interval and duration | +| | | Preferred unit: micromole per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/gaseous_substances.md b/mixs6/gaseous_substances.md new file mode 100644 index 00000000..a079a219 --- /dev/null +++ b/mixs6/gaseous_substances.md @@ -0,0 +1,48 @@ + +# Slot: gaseous_substances + + +Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + +URI: [mixs.vocab:gaseous_substances](https://w3id.org/mixs/vocab/gaseous_substances) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gaseous substances | +| **Mappings:** | | MIXS:0000661 | +| **Comments:** | | Expected value: gaseous substance name;measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/gastrointest_disord.md b/mixs6/gastrointest_disord.md new file mode 100644 index 00000000..486cb287 --- /dev/null +++ b/mixs6/gastrointest_disord.md @@ -0,0 +1,47 @@ + +# Slot: gastrointest_disord + + +History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + +URI: [mixs.vocab:gastrointest_disord](https://w3id.org/mixs/vocab/gastrointest_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gastrointestinal tract disorder | +| **Mappings:** | | MIXS:0000280 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: human-gut | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/gender_restroom.md b/mixs6/gender_restroom.md new file mode 100644 index 00000000..772290ac --- /dev/null +++ b/mixs6/gender_restroom.md @@ -0,0 +1,47 @@ + +# Slot: gender_restroom + + +The gender type of the restroom + +URI: [mixs.vocab:gender_restroom](https://w3id.org/mixs/vocab/gender_restroom) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gender of restroom | +| **Mappings:** | | MIXS:0000808 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 80.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='male', description=None) | + diff --git a/mixs6/genetic_mod.md b/mixs6/genetic_mod.md new file mode 100644 index 00000000..6bc37490 --- /dev/null +++ b/mixs6/genetic_mod.md @@ -0,0 +1,59 @@ + +# Slot: genetic_mod + + +Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + +URI: [mixs.vocab:genetic_mod](https://w3id.org/mixs/vocab/genetic_mod) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | genetic modification | +| **Mappings:** | | MIXS:0000859 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Occurrence: 1 | +| | | Position: 3.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='aox1A transgenic', description=None) | + diff --git a/mixs6/geo_loc_name.md b/mixs6/geo_loc_name.md new file mode 100644 index 00000000..09dc636a --- /dev/null +++ b/mixs6/geo_loc_name.md @@ -0,0 +1,249 @@ + +# Slot: geo_loc_name + + +The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + +URI: [mixs.vocab:geo_loc_name](https://w3id.org/mixs/vocab/geo_loc_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + * [ME➞geo_loc_name](ME_geo_loc_name.md) + * [MIGS bacteria➞geo_loc_name](MIGS_bacteria_geo_loc_name.md) + * [MIGS eukaryote➞geo_loc_name](MIGS_eukaryote_geo_loc_name.md) + * [MIGS org➞geo_loc_name](MIGS_org_geo_loc_name.md) + * [MIGS plant➞geo_loc_name](MIGS_plant_geo_loc_name.md) + * [MIGS virus➞geo_loc_name](MIGS_virus_geo_loc_name.md) + * [MIMAG➞geo_loc_name](MIMAG_geo_loc_name.md) + * [MIMARKS specimen➞geo_loc_name](MIMARKS_specimen_geo_loc_name.md) + * [MIMARKS survey➞geo_loc_name](MIMARKS_survey_geo_loc_name.md) + * [MISAG➞geo_loc_name](MISAG_geo_loc_name.md) + * [MIUVIG➞geo_loc_name](MIUVIG_geo_loc_name.md) + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | geographic location (country and/or sea,region) | +| **Comments:** | | Expected value: country or sea name (INSDC or GAZ);region(GAZ);specific location name | +| | | Position: 8.0 | +| **Examples:** | | Example(value='Germany;North Rhine-Westphalia;Eifel National Park', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/17 | + diff --git a/mixs6/gestation_state.md b/mixs6/gestation_state.md new file mode 100644 index 00000000..9e2c7046 --- /dev/null +++ b/mixs6/gestation_state.md @@ -0,0 +1,47 @@ + +# Slot: gestation_state + + +Specification of the gestation state + +URI: [mixs.vocab:gestation_state](https://w3id.org/mixs/vocab/gestation_state) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/gestation state | +| **Mappings:** | | MIXS:0000272 | +| **Comments:** | | Expected value: gestation state | +| | | Occurrence: 1 | +| | | Position: 36.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/glucosidase_act.md b/mixs6/glucosidase_act.md new file mode 100644 index 00000000..ee1c35fb --- /dev/null +++ b/mixs6/glucosidase_act.md @@ -0,0 +1,72 @@ + +# Slot: glucosidase_act + + +Measurement of glucosidase activity + +URI: [mixs.vocab:glucosidase_act](https://w3id.org/mixs/vocab/glucosidase_act) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | glucosidase activity | +| **Mappings:** | | MIXS:0000137 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mol per liter per hour | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='5 mol per liter per hour', description=None) | + diff --git a/mixs6/gravidity.md b/mixs6/gravidity.md new file mode 100644 index 00000000..6c55585e --- /dev/null +++ b/mixs6/gravidity.md @@ -0,0 +1,47 @@ + +# Slot: gravidity + + +Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + +URI: [mixs.vocab:gravidity](https://w3id.org/mixs/vocab/gravidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gravidity | +| **Mappings:** | | MIXS:0000875 | +| **Comments:** | | Expected value: gravidity status;timestamp | +| | | Occurrence: 1 | +| | | Position: 35.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='yes;due date:2018-05-11', description=None) | + diff --git a/mixs6/gravity.md b/mixs6/gravity.md new file mode 100644 index 00000000..4c3e2c5c --- /dev/null +++ b/mixs6/gravity.md @@ -0,0 +1,48 @@ + +# Slot: gravity + + +Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + +URI: [mixs.vocab:gravity](https://w3id.org/mixs/vocab/gravity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gravity | +| **Mappings:** | | MIXS:0000559 | +| **Comments:** | | Expected value: gravity factor value;treatment interval and duration | +| | | Preferred unit: meter per square second, g | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/growth_facil.md b/mixs6/growth_facil.md new file mode 100644 index 00000000..73a66397 --- /dev/null +++ b/mixs6/growth_facil.md @@ -0,0 +1,47 @@ + +# Slot: growth_facil + + +Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + +URI: [mixs.vocab:growth_facil](https://w3id.org/mixs/vocab/growth_facil) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | growth facility | +| **Mappings:** | | MIXS:0001043 | +| **Comments:** | | Expected value: free text or CO | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='Growth chamber [CO_715:0000189]', description=None) | + diff --git a/mixs6/growth_habit.md b/mixs6/growth_habit.md new file mode 100644 index 00000000..84c7ba02 --- /dev/null +++ b/mixs6/growth_habit.md @@ -0,0 +1,47 @@ + +# Slot: growth_habit + + +Characteristic shape, appearance or growth form of a plant species + +URI: [mixs.vocab:growth_habit](https://w3id.org/mixs/vocab/growth_habit) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | growth habit | +| **Mappings:** | | MIXS:0001044 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='spreading', description=None) | + diff --git a/mixs6/growth_hormone_regm.md b/mixs6/growth_hormone_regm.md new file mode 100644 index 00000000..d281763e --- /dev/null +++ b/mixs6/growth_hormone_regm.md @@ -0,0 +1,48 @@ + +# Slot: growth_hormone_regm + + +Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + +URI: [mixs.vocab:growth_hormone_regm](https://w3id.org/mixs/vocab/growth_hormone_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | growth hormone regimen | +| **Mappings:** | | MIXS:0000560 | +| **Comments:** | | Expected value: growth hormone name;growth hormone amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/gynecologic_disord.md b/mixs6/gynecologic_disord.md new file mode 100644 index 00000000..8d988444 --- /dev/null +++ b/mixs6/gynecologic_disord.md @@ -0,0 +1,47 @@ + +# Slot: gynecologic_disord + + +History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + +URI: [mixs.vocab:gynecologic_disord](https://w3id.org/mixs/vocab/gynecologic_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gynecological disorder | +| **Mappings:** | | MIXS:0000288 | +| **Comments:** | | Expected value: gynecological disorder | +| | | Occurrence: m | +| | | Position: 9.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/hall_count.md b/mixs6/hall_count.md new file mode 100644 index 00000000..31e4d54c --- /dev/null +++ b/mixs6/hall_count.md @@ -0,0 +1,47 @@ + +# Slot: hall_count + + +The total count of hallways and cooridors in the built structure + +URI: [mixs.vocab:hall_count](https://w3id.org/mixs/vocab/hall_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hallway/corridor count | +| **Mappings:** | | MIXS:0000228 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 81.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/handidness.md b/mixs6/handidness.md new file mode 100644 index 00000000..61c5a807 --- /dev/null +++ b/mixs6/handidness.md @@ -0,0 +1,47 @@ + +# Slot: handidness + + +The handidness of the individual sampled + +URI: [mixs.vocab:handidness](https://w3id.org/mixs/vocab/handidness) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | handidness | +| **Mappings:** | | MIXS:0000809 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 82.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='right handedness', description=None) | + diff --git a/mixs6/hc_produced.md b/mixs6/hc_produced.md new file mode 100644 index 00000000..730e2423 --- /dev/null +++ b/mixs6/hc_produced.md @@ -0,0 +1,59 @@ + +# Slot: hc_produced + + +Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:hc_produced](https://w3id.org/mixs/vocab/hc_produced) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon type produced | +| **Mappings:** | | MIXS:0000989 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 2.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Gas', description=None) | + diff --git a/mixs6/hcr.md b/mixs6/hcr.md new file mode 100644 index 00000000..548eb929 --- /dev/null +++ b/mixs6/hcr.md @@ -0,0 +1,59 @@ + +# Slot: hcr + + +Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:hcr](https://w3id.org/mixs/vocab/hcr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource type | +| **Mappings:** | | MIXS:0000988 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Oil Sand', description=None) | + diff --git a/mixs6/hcr_fw_salinity.md b/mixs6/hcr_fw_salinity.md new file mode 100644 index 00000000..7ecac56f --- /dev/null +++ b/mixs6/hcr_fw_salinity.md @@ -0,0 +1,60 @@ + +# Slot: hcr_fw_salinity + + +Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + +URI: [mixs.vocab:hcr_fw_salinity](https://w3id.org/mixs/vocab/hcr_fw_salinity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | formation water salinity | +| **Mappings:** | | MIXS:0000406 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 16.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/hcr_geol_age.md b/mixs6/hcr_geol_age.md new file mode 100644 index 00000000..7100eb7a --- /dev/null +++ b/mixs6/hcr_geol_age.md @@ -0,0 +1,59 @@ + +# Slot: hcr_geol_age + + +Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:hcr_geol_age](https://w3id.org/mixs/vocab/hcr_geol_age) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource geological age | +| **Mappings:** | | MIXS:0000993 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 14.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Silurian', description=None) | + diff --git a/mixs6/hcr_pressure.md b/mixs6/hcr_pressure.md new file mode 100644 index 00000000..8130baa5 --- /dev/null +++ b/mixs6/hcr_pressure.md @@ -0,0 +1,60 @@ + +# Slot: hcr_pressure + + +Original pressure of the hydrocarbon resource + +URI: [mixs.vocab:hcr_pressure](https://w3id.org/mixs/vocab/hcr_pressure) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource original pressure | +| **Mappings:** | | MIXS:0000395 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: atmosphere, kilopascal | +| | | Occurrence: 1 | +| | | Position: 8.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/hcr_temp.md b/mixs6/hcr_temp.md new file mode 100644 index 00000000..1bb2dfe5 --- /dev/null +++ b/mixs6/hcr_temp.md @@ -0,0 +1,60 @@ + +# Slot: hcr_temp + + +Original temperature of the hydrocarbon resource + +URI: [mixs.vocab:hcr_temp](https://w3id.org/mixs/vocab/hcr_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource original temperature | +| **Mappings:** | | MIXS:0000393 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 6.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='150-295 degree Celsius', description=None) | + diff --git a/mixs6/health_disease_stat.md b/mixs6/health_disease_stat.md new file mode 100644 index 00000000..c269af6b --- /dev/null +++ b/mixs6/health_disease_stat.md @@ -0,0 +1,36 @@ + +# Slot: health_disease_stat + + +Health or disease status of specific host at time of collection + +URI: [mixs.vocab:health_disease_stat](https://w3id.org/mixs/vocab/health_disease_stat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | health or disease status of specific host at time of collection | +| **Comments:** | | Expected value: enumeration | +| | | Position: 25.0 | +| **Examples:** | | Example(value='dead', description=None) | + diff --git a/mixs6/heat_cool_type.md b/mixs6/heat_cool_type.md new file mode 100644 index 00000000..898f151e --- /dev/null +++ b/mixs6/heat_cool_type.md @@ -0,0 +1,47 @@ + +# Slot: heat_cool_type + + +Methods of conditioning or heating a room or building + +URI: [mixs.vocab:heat_cool_type](https://w3id.org/mixs/vocab/heat_cool_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating and cooling system type | +| **Mappings:** | | MIXS:0000766 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 18.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='heat pump', description=None) | + diff --git a/mixs6/heat_deliv_loc.md b/mixs6/heat_deliv_loc.md new file mode 100644 index 00000000..87859c31 --- /dev/null +++ b/mixs6/heat_deliv_loc.md @@ -0,0 +1,47 @@ + +# Slot: heat_deliv_loc + + +The location of heat delivery within the room + +URI: [mixs.vocab:heat_deliv_loc](https://w3id.org/mixs/vocab/heat_deliv_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating delivery locations | +| **Mappings:** | | MIXS:0000810 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 83.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='north', description=None) | + diff --git a/mixs6/heat_system_deliv_meth.md b/mixs6/heat_system_deliv_meth.md new file mode 100644 index 00000000..6123ad24 --- /dev/null +++ b/mixs6/heat_system_deliv_meth.md @@ -0,0 +1,47 @@ + +# Slot: heat_system_deliv_meth + + +The method by which the heat is delivered through the system + +URI: [mixs.vocab:heat_system_deliv_meth](https://w3id.org/mixs/vocab/heat_system_deliv_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating system delivery method | +| **Mappings:** | | MIXS:0000812 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 84.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='radiant', description=None) | + diff --git a/mixs6/heat_system_id.md b/mixs6/heat_system_id.md new file mode 100644 index 00000000..398c1fb0 --- /dev/null +++ b/mixs6/heat_system_id.md @@ -0,0 +1,47 @@ + +# Slot: heat_system_id + + +The heating system identifier + +URI: [mixs.vocab:heat_system_id](https://w3id.org/mixs/vocab/heat_system_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating system identifier | +| **Mappings:** | | MIXS:0000833 | +| **Comments:** | | Expected value: unique identifier | +| | | Occurrence: 1 | +| | | Position: 85.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/heavy_metals.md b/mixs6/heavy_metals.md new file mode 100644 index 00000000..936fb920 --- /dev/null +++ b/mixs6/heavy_metals.md @@ -0,0 +1,48 @@ + +# Slot: heavy_metals + + +Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + +URI: [mixs.vocab:heavy_metals](https://w3id.org/mixs/vocab/heavy_metals) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/heavy metals | +| **Mappings:** | | MIXS:0000652 | +| **Comments:** | | Expected value: heavy metal name;measurement value | +| | | Preferred unit: microgram per gram | +| | | Occurrence: m | +| | | Position: 48.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/heavy_metals_meth.md b/mixs6/heavy_metals_meth.md new file mode 100644 index 00000000..1c42a529 --- /dev/null +++ b/mixs6/heavy_metals_meth.md @@ -0,0 +1,47 @@ + +# Slot: heavy_metals_meth + + +Reference or method used in determining heavy metals + +URI: [mixs.vocab:heavy_metals_meth](https://w3id.org/mixs/vocab/heavy_metals_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/heavy metals method | +| **Mappings:** | | MIXS:0000343 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 49.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/height_carper_fiber.md b/mixs6/height_carper_fiber.md new file mode 100644 index 00000000..a4e7e7ce --- /dev/null +++ b/mixs6/height_carper_fiber.md @@ -0,0 +1,48 @@ + +# Slot: height_carper_fiber + + +The average carpet fiber height in the indoor environment + +URI: [mixs.vocab:height_carper_fiber](https://w3id.org/mixs/vocab/height_carper_fiber) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | height carpet fiber mat | +| **Mappings:** | | MIXS:0000167 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: centimeter | +| | | Occurrence: 1 | +| | | Position: 86.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/herbicide_regm.md b/mixs6/herbicide_regm.md new file mode 100644 index 00000000..d94ee4cd --- /dev/null +++ b/mixs6/herbicide_regm.md @@ -0,0 +1,48 @@ + +# Slot: herbicide_regm + + +Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:herbicide_regm](https://w3id.org/mixs/vocab/herbicide_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | herbicide regimen | +| **Mappings:** | | MIXS:0000561 | +| **Comments:** | | Expected value: herbicide name;herbicide amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/horizon.md b/mixs6/horizon.md new file mode 100644 index 00000000..cf2fdaad --- /dev/null +++ b/mixs6/horizon.md @@ -0,0 +1,47 @@ + +# Slot: horizon + + +Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + +URI: [mixs.vocab:horizon](https://w3id.org/mixs/vocab/horizon) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | horizon | +| **Mappings:** | | MIXS:0001082 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 12.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='A horizon', description=None) | + diff --git a/mixs6/horizon_meth.md b/mixs6/horizon_meth.md new file mode 100644 index 00000000..a1c729fc --- /dev/null +++ b/mixs6/horizon_meth.md @@ -0,0 +1,47 @@ + +# Slot: horizon_meth + + +Reference or method used in determining the horizon + +URI: [mixs.vocab:horizon_meth](https://w3id.org/mixs/vocab/horizon_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | horizon method | +| **Mappings:** | | MIXS:0000321 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 13.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_age.md b/mixs6/host_age.md new file mode 100644 index 00000000..c5ce9f0e --- /dev/null +++ b/mixs6/host_age.md @@ -0,0 +1,120 @@ + +# Slot: host_age + + +Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + +URI: [mixs.vocab:host_age](https://w3id.org/mixs/vocab/host_age) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host age | +| **Mappings:** | | MIXS:0000255 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: year, day, hour | +| | | Occurrence: 1 | +| | | Position: 9.0 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='10 days', description=None) | + diff --git a/mixs6/host_blood_press_diast.md b/mixs6/host_blood_press_diast.md new file mode 100644 index 00000000..6f6c1207 --- /dev/null +++ b/mixs6/host_blood_press_diast.md @@ -0,0 +1,48 @@ + +# Slot: host_blood_press_diast + + +Resting diastolic blood pressure, measured as mm mercury + +URI: [mixs.vocab:host_blood_press_diast](https://w3id.org/mixs/vocab/host_blood_press_diast) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host blood pressure diastolic | +| **Mappings:** | | MIXS:0000258 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter mercury | +| | | Occurrence: 1 | +| | | Position: 31.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_blood_press_syst.md b/mixs6/host_blood_press_syst.md new file mode 100644 index 00000000..06d9888a --- /dev/null +++ b/mixs6/host_blood_press_syst.md @@ -0,0 +1,48 @@ + +# Slot: host_blood_press_syst + + +Resting systolic blood pressure, measured as mm mercury + +URI: [mixs.vocab:host_blood_press_syst](https://w3id.org/mixs/vocab/host_blood_press_syst) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host blood pressure systolic | +| **Mappings:** | | MIXS:0000259 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter mercury | +| | | Occurrence: 1 | +| | | Position: 32.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_body_habitat.md b/mixs6/host_body_habitat.md new file mode 100644 index 00000000..f7fcb755 --- /dev/null +++ b/mixs6/host_body_habitat.md @@ -0,0 +1,47 @@ + +# Slot: host_body_habitat + + +Original body habitat where the sample was obtained from + +URI: [mixs.vocab:host_body_habitat](https://w3id.org/mixs/vocab/host_body_habitat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body habitat | +| **Mappings:** | | MIXS:0000866 | +| **Comments:** | | Expected value: free text | +| | | Occurrence: 1 | +| | | Position: 14.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='nasopharynx', description=None) | + diff --git a/mixs6/host_body_mass_index.md b/mixs6/host_body_mass_index.md new file mode 100644 index 00000000..5822e2bd --- /dev/null +++ b/mixs6/host_body_mass_index.md @@ -0,0 +1,96 @@ + +# Slot: host_body_mass_index + + +Body mass index, calculated as weight/(height)squared + +URI: [mixs.vocab:host_body_mass_index](https://w3id.org/mixs/vocab/host_body_mass_index) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body-mass index | +| **Mappings:** | | MIXS:0000317 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram per square meter | +| | | Occurrence: 1 | +| | | Position: 20.0 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='22 kilogram per square meter', description=None) | + diff --git a/mixs6/host_body_product.md b/mixs6/host_body_product.md new file mode 100644 index 00000000..6bd1a45b --- /dev/null +++ b/mixs6/host_body_product.md @@ -0,0 +1,107 @@ + +# Slot: host_body_product + + +Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + +URI: [mixs.vocab:host_body_product](https://w3id.org/mixs/vocab/host_body_product) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body product | +| **Mappings:** | | MIXS:0000888 | +| **Comments:** | | Expected value: FMA or UBERON | +| | | Occurrence: 1 | +| | | Position: 16.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='Portion of mucus [fma66938]', description=None) | + diff --git a/mixs6/host_body_site.md b/mixs6/host_body_site.md new file mode 100644 index 00000000..ac527c7a --- /dev/null +++ b/mixs6/host_body_site.md @@ -0,0 +1,107 @@ + +# Slot: host_body_site + + +Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + +URI: [mixs.vocab:host_body_site](https://w3id.org/mixs/vocab/host_body_site) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body site | +| **Mappings:** | | MIXS:0000867 | +| **Comments:** | | Expected value: FMA or UBERON | +| | | Occurrence: 1 | +| | | Position: 15.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='gill [UBERON:0002535]', description=None) | + diff --git a/mixs6/host_body_temp.md b/mixs6/host_body_temp.md new file mode 100644 index 00000000..09964e25 --- /dev/null +++ b/mixs6/host_body_temp.md @@ -0,0 +1,108 @@ + +# Slot: host_body_temp + + +Core body temperature of the host when sample was collected + +URI: [mixs.vocab:host_body_temp](https://w3id.org/mixs/vocab/host_body_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body temperature | +| **Mappings:** | | MIXS:0000274 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 29.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='15 degree Celsius', description=None) | + diff --git a/mixs6/host_color.md b/mixs6/host_color.md new file mode 100644 index 00000000..e82a6612 --- /dev/null +++ b/mixs6/host_color.md @@ -0,0 +1,47 @@ + +# Slot: host_color + + +The color of host + +URI: [mixs.vocab:host_color](https://w3id.org/mixs/vocab/host_color) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host color | +| **Mappings:** | | MIXS:0000260 | +| **Comments:** | | Expected value: color | +| | | Occurrence: 1 | +| | | Position: 33.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_common_name.md b/mixs6/host_common_name.md new file mode 100644 index 00000000..ddced188 --- /dev/null +++ b/mixs6/host_common_name.md @@ -0,0 +1,59 @@ + +# Slot: host_common_name + + +Common name of the host, e.g. Human + +URI: [mixs.vocab:host_common_name](https://w3id.org/mixs/vocab/host_common_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host common name | +| **Mappings:** | | MIXS:0000248 | +| **Comments:** | | Expected value: common name | +| | | Occurrence: 1 | +| | | Position: 4.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='mussel', description=None) | + diff --git a/mixs6/host_diet.md b/mixs6/host_diet.md new file mode 100644 index 00000000..dc87246d --- /dev/null +++ b/mixs6/host_diet.md @@ -0,0 +1,107 @@ + +# Slot: host_diet + + +Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + +URI: [mixs.vocab:host_diet](https://w3id.org/mixs/vocab/host_diet) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host diet | +| **Mappings:** | | MIXS:0000869 | +| **Comments:** | | Expected value: diet type | +| | | Occurrence: m | +| | | Position: 20.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='herbivore', description=None) | + diff --git a/mixs6/host_disease_stat.md b/mixs6/host_disease_stat.md new file mode 100644 index 00000000..e70890e9 --- /dev/null +++ b/mixs6/host_disease_stat.md @@ -0,0 +1,119 @@ + +# Slot: host_disease_stat + + +List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + +URI: [mixs.vocab:host_disease_stat](https://w3id.org/mixs/vocab/host_disease_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host disease status | +| **Mappings:** | | MIXS:0000031 | +| **Comments:** | | Expected value: disease name or DO | +| | | Occurrence: m | +| | | Position: 12.0 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='rabies [DOID:11260]', description=None) | + diff --git a/mixs6/host_dry_mass.md b/mixs6/host_dry_mass.md new file mode 100644 index 00000000..84b93496 --- /dev/null +++ b/mixs6/host_dry_mass.md @@ -0,0 +1,60 @@ + +# Slot: host_dry_mass + + +Measurement of dry mass + +URI: [mixs.vocab:host_dry_mass](https://w3id.org/mixs/vocab/host_dry_mass) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host dry mass | +| **Mappings:** | | MIXS:0000257 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 30.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='500 gram', description=None) | + diff --git a/mixs6/host_family_relationship.md b/mixs6/host_family_relationship.md new file mode 100644 index 00000000..792a5e91 --- /dev/null +++ b/mixs6/host_family_relationship.md @@ -0,0 +1,107 @@ + +# Slot: host_family_relationship + + +Relationships to other hosts in the same study; can include multiple relationships + +URI: [mixs.vocab:host_family_relationship](https://w3id.org/mixs/vocab/host_family_relationship) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host family relationship | +| **Mappings:** | | MIXS:0000872 | +| **Comments:** | | Expected value: relationship type;arbitrary identifier | +| | | Occurrence: m | +| | | Position: 24.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='offspring;Mussel25', description=None) | + diff --git a/mixs6/host_genotype.md b/mixs6/host_genotype.md new file mode 100644 index 00000000..b104145f --- /dev/null +++ b/mixs6/host_genotype.md @@ -0,0 +1,119 @@ + +# Slot: host_genotype + + +Observed genotype + +URI: [mixs.vocab:host_genotype](https://w3id.org/mixs/vocab/host_genotype) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host genotype | +| **Mappings:** | | MIXS:0000365 | +| **Comments:** | | Expected value: genotype | +| | | Occurrence: 1 | +| | | Position: 27.0 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='C57BL/6', description=None) | + diff --git a/mixs6/host_growth_cond.md b/mixs6/host_growth_cond.md new file mode 100644 index 00000000..ff0a887e --- /dev/null +++ b/mixs6/host_growth_cond.md @@ -0,0 +1,47 @@ + +# Slot: host_growth_cond + + +Literature reference giving growth conditions of the host + +URI: [mixs.vocab:host_growth_cond](https://w3id.org/mixs/vocab/host_growth_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host growth conditions | +| **Mappings:** | | MIXS:0000871 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Occurrence: 1 | +| | | Position: 22.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='https://academic.oup.com/icesjms/article/68/2/349/617247', description=None) | + diff --git a/mixs6/host_height.md b/mixs6/host_height.md new file mode 100644 index 00000000..7d0578f3 --- /dev/null +++ b/mixs6/host_height.md @@ -0,0 +1,120 @@ + +# Slot: host_height + + +The height of subject + +URI: [mixs.vocab:host_height](https://w3id.org/mixs/vocab/host_height) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host height | +| **Mappings:** | | MIXS:0000264 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: centimeter, millimeter, meter | +| | | Occurrence: 1 | +| | | Position: 18.0 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='0.1 meter', description=None) | + diff --git a/mixs6/host_hiv_stat.md b/mixs6/host_hiv_stat.md new file mode 100644 index 00000000..69c59820 --- /dev/null +++ b/mixs6/host_hiv_stat.md @@ -0,0 +1,47 @@ + +# Slot: host_hiv_stat + + +HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + +URI: [mixs.vocab:host_hiv_stat](https://w3id.org/mixs/vocab/host_hiv_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host HIV status | +| **Mappings:** | | MIXS:0000265 | +| **Comments:** | | Expected value: HIV status;HAART initiation status | +| | | Occurrence: 1 | +| | | Position: 18.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes;yes', description=None) | + diff --git a/mixs6/host_infra_specific_name.md b/mixs6/host_infra_specific_name.md new file mode 100644 index 00000000..3590705c --- /dev/null +++ b/mixs6/host_infra_specific_name.md @@ -0,0 +1,59 @@ + +# Slot: host_infra_specific_name + + +Taxonomic information about the host below subspecies level + +URI: [mixs.vocab:host_infra_specific_name](https://w3id.org/mixs/vocab/host_infra_specific_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host infra-specific name | +| **Mappings:** | | MIXS:0000253 | +| **Comments:** | | Expected value: name | +| | | Occurrence: 1 | +| | | Position: 25.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='borealis', description=None) | + diff --git a/mixs6/host_infra_specific_rank.md b/mixs6/host_infra_specific_rank.md new file mode 100644 index 00000000..0d71f079 --- /dev/null +++ b/mixs6/host_infra_specific_rank.md @@ -0,0 +1,59 @@ + +# Slot: host_infra_specific_rank + + +Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + +URI: [mixs.vocab:host_infra_specific_rank](https://w3id.org/mixs/vocab/host_infra_specific_rank) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host infra-specific rank | +| **Mappings:** | | MIXS:0000254 | +| **Comments:** | | Expected value: rank | +| | | Occurrence: 1 | +| | | Position: 26.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='subspecies', description=None) | + diff --git a/mixs6/host_last_meal.md b/mixs6/host_last_meal.md new file mode 100644 index 00000000..956f7f2d --- /dev/null +++ b/mixs6/host_last_meal.md @@ -0,0 +1,107 @@ + +# Slot: host_last_meal + + +Content of last meal and time since feeding; can include multiple values + +URI: [mixs.vocab:host_last_meal](https://w3id.org/mixs/vocab/host_last_meal) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host last meal | +| **Mappings:** | | MIXS:0000870 | +| **Comments:** | | Expected value: content;duration | +| | | Occurrence: m | +| | | Position: 21.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='corn feed;P2H', description=None) | + diff --git a/mixs6/host_length.md b/mixs6/host_length.md new file mode 100644 index 00000000..2422cc87 --- /dev/null +++ b/mixs6/host_length.md @@ -0,0 +1,60 @@ + +# Slot: host_length + + +The length of subject + +URI: [mixs.vocab:host_length](https://w3id.org/mixs/vocab/host_length) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host length | +| **Mappings:** | | MIXS:0000256 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: centimeter, millimeter, meter | +| | | Occurrence: 1 | +| | | Position: 19.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='1 meter', description=None) | + diff --git a/mixs6/host_life_stage.md b/mixs6/host_life_stage.md new file mode 100644 index 00000000..c4089d97 --- /dev/null +++ b/mixs6/host_life_stage.md @@ -0,0 +1,59 @@ + +# Slot: host_life_stage + + +Description of life stage of host + +URI: [mixs.vocab:host_life_stage](https://w3id.org/mixs/vocab/host_life_stage) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host life stage | +| **Mappings:** | | MIXS:0000251 | +| **Comments:** | | Expected value: stage | +| | | Occurrence: 1 | +| | | Position: 10.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='adult', description=None) | + diff --git a/mixs6/host_occupation.md b/mixs6/host_occupation.md new file mode 100644 index 00000000..d1ddc1fe --- /dev/null +++ b/mixs6/host_occupation.md @@ -0,0 +1,95 @@ + +# Slot: host_occupation + + +Most frequent job performed by subject + +URI: [mixs.vocab:host_occupation](https://w3id.org/mixs/vocab/host_occupation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host occupation | +| **Mappings:** | | MIXS:0000896 | +| **Comments:** | | Expected value: IHMC code | +| | | Occurrence: 1 | +| | | Position: 24.0 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='veterinary', description=None) | + diff --git a/mixs6/host_phenotype.md b/mixs6/host_phenotype.md new file mode 100644 index 00000000..2ba2d358 --- /dev/null +++ b/mixs6/host_phenotype.md @@ -0,0 +1,119 @@ + +# Slot: host_phenotype + + +Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + +URI: [mixs.vocab:host_phenotype](https://w3id.org/mixs/vocab/host_phenotype) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host phenotype | +| **Mappings:** | | MIXS:0000874 | +| **Comments:** | | Expected value: PATO or HP | +| | | Occurrence: 1 | +| | | Position: 28.0 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='elongated [PATO:0001154]', description=None) | + diff --git a/mixs6/host_pred_appr.md b/mixs6/host_pred_appr.md new file mode 100644 index 00000000..81696362 --- /dev/null +++ b/mixs6/host_pred_appr.md @@ -0,0 +1,34 @@ + +# Slot: host_pred_appr + + +Tool or approach used for host prediction + +URI: [mixs.vocab:host_pred_appr](https://w3id.org/mixs/vocab/host_pred_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host prediction approach | +| **Comments:** | | Expected value: enumeration | +| | | Position: 90.0 | +| **Examples:** | | Example(value='CRISPR spacer match', description=None) | + diff --git a/mixs6/host_pred_est_acc.md b/mixs6/host_pred_est_acc.md new file mode 100644 index 00000000..3738cc6f --- /dev/null +++ b/mixs6/host_pred_est_acc.md @@ -0,0 +1,34 @@ + +# Slot: host_pred_est_acc + + +For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + +URI: [mixs.vocab:host_pred_est_acc](https://w3id.org/mixs/vocab/host_pred_est_acc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host prediction estimated accuracy | +| **Comments:** | | Expected value: false discovery rate | +| | | Position: 91.0 | +| **Examples:** | | Example(value='CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)', description=None) | + diff --git a/mixs6/host_pulse.md b/mixs6/host_pulse.md new file mode 100644 index 00000000..38c32af4 --- /dev/null +++ b/mixs6/host_pulse.md @@ -0,0 +1,96 @@ + +# Slot: host_pulse + + +Resting pulse, measured as beats per minute + +URI: [mixs.vocab:host_pulse](https://w3id.org/mixs/vocab/host_pulse) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host pulse | +| **Mappings:** | | MIXS:0000333 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: beats per minute | +| | | Occurrence: 1 | +| | | Position: 35.0 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='65 beats per minute', description=None) | + diff --git a/mixs6/host_sex.md b/mixs6/host_sex.md new file mode 100644 index 00000000..4be83934 --- /dev/null +++ b/mixs6/host_sex.md @@ -0,0 +1,107 @@ + +# Slot: host_sex + + +Physical sex of the host + +URI: [mixs.vocab:host_sex](https://w3id.org/mixs/vocab/host_sex) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host sex | +| **Mappings:** | | MIXS:0000811 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 11.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='female', description=None) | + diff --git a/mixs6/host_shape.md b/mixs6/host_shape.md new file mode 100644 index 00000000..5bcb39a4 --- /dev/null +++ b/mixs6/host_shape.md @@ -0,0 +1,47 @@ + +# Slot: host_shape + + +Morphological shape of host + +URI: [mixs.vocab:host_shape](https://w3id.org/mixs/vocab/host_shape) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host shape | +| **Mappings:** | | MIXS:0000261 | +| **Comments:** | | Expected value: shape | +| | | Occurrence: 1 | +| | | Position: 34.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='round', description=None) | + diff --git a/mixs6/host_spec_range.md b/mixs6/host_spec_range.md new file mode 100644 index 00000000..a3d13af8 --- /dev/null +++ b/mixs6/host_spec_range.md @@ -0,0 +1,39 @@ + +# Slot: host_spec_range + + +The NCBI taxonomy identifier of the specific host if it is known + +URI: [mixs.vocab:host_spec_range](https://w3id.org/mixs/vocab/host_spec_range) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host specificity or range | +| **Comments:** | | Expected value: NCBI taxid | +| | | Position: 24.0 | +| **Examples:** | | Example(value='9606', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/66 | + diff --git a/mixs6/host_subject_id.md b/mixs6/host_subject_id.md new file mode 100644 index 00000000..f7b59b74 --- /dev/null +++ b/mixs6/host_subject_id.md @@ -0,0 +1,107 @@ + +# Slot: host_subject_id + + +A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + +URI: [mixs.vocab:host_subject_id](https://w3id.org/mixs/vocab/host_subject_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host subject id | +| **Mappings:** | | MIXS:0000861 | +| **Comments:** | | Expected value: unique identifier | +| | | Occurrence: 1 | +| | | Position: 8.0 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='MPI123', description=None) | + diff --git a/mixs6/host_substrate.md b/mixs6/host_substrate.md new file mode 100644 index 00000000..fe8647e8 --- /dev/null +++ b/mixs6/host_substrate.md @@ -0,0 +1,47 @@ + +# Slot: host_substrate + + +The growth substrate of the host + +URI: [mixs.vocab:host_substrate](https://w3id.org/mixs/vocab/host_substrate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host substrate | +| **Mappings:** | | MIXS:0000252 | +| **Comments:** | | Expected value: substrate name | +| | | Occurrence: 1 | +| | | Position: 23.0 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='rock', description=None) | + diff --git a/mixs6/host_symbiont.md b/mixs6/host_symbiont.md new file mode 100644 index 00000000..9eb46abb --- /dev/null +++ b/mixs6/host_symbiont.md @@ -0,0 +1,117 @@ + +# Slot: host_symbiont + + +The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + +URI: [mixs.vocab:host_symbiont](https://w3id.org/mixs/vocab/host_symbiont) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | observed host symbionts | +| **Comments:** | | Expected value: species name or common name | +| | | Occurrence: m | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='flukeworms', description=None) | + diff --git a/mixs6/host_taxid.md b/mixs6/host_taxid.md new file mode 100644 index 00000000..b9708a09 --- /dev/null +++ b/mixs6/host_taxid.md @@ -0,0 +1,59 @@ + +# Slot: host_taxid + + +NCBI taxon id of the host, e.g. 9606 + +URI: [mixs.vocab:host_taxid](https://w3id.org/mixs/vocab/host_taxid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host taxid | +| **Mappings:** | | MIXS:0000250 | +| **Comments:** | | Expected value: NCBI taxon identifier | +| | | Occurrence: 1 | +| | | Position: 7.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='7955', description=None) | + diff --git a/mixs6/host_tot_mass.md b/mixs6/host_tot_mass.md new file mode 100644 index 00000000..699df932 --- /dev/null +++ b/mixs6/host_tot_mass.md @@ -0,0 +1,120 @@ + +# Slot: host_tot_mass + + +Total mass of the host at collection, the unit depends on host + +URI: [mixs.vocab:host_tot_mass](https://w3id.org/mixs/vocab/host_tot_mass) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host total mass | +| **Mappings:** | | MIXS:0000263 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 17.0 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='2500 gram', description=None) | + diff --git a/mixs6/host_wet_mass.md b/mixs6/host_wet_mass.md new file mode 100644 index 00000000..1e0f2d97 --- /dev/null +++ b/mixs6/host_wet_mass.md @@ -0,0 +1,48 @@ + +# Slot: host_wet_mass + + +Measurement of wet mass + +URI: [mixs.vocab:host_wet_mass](https://w3id.org/mixs/vocab/host_wet_mass) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host wet mass | +| **Mappings:** | | MIXS:0000567 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='1500 gram', description=None) | + diff --git a/mixs6/hrt.md b/mixs6/hrt.md new file mode 100644 index 00000000..413bbc93 --- /dev/null +++ b/mixs6/hrt.md @@ -0,0 +1,47 @@ + +# Slot: hrt + + +Whether subject had hormone replacement theraphy, and if yes start date + +URI: [mixs.vocab:hrt](https://w3id.org/mixs/vocab/hrt) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | HRT | +| **Mappings:** | | MIXS:0000969 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 7.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/humidity.md b/mixs6/humidity.md new file mode 100644 index 00000000..bc036ab1 --- /dev/null +++ b/mixs6/humidity.md @@ -0,0 +1,48 @@ + +# Slot: humidity + + +Amount of water vapour in the air, at the time of sampling + +URI: [mixs.vocab:humidity](https://w3id.org/mixs/vocab/humidity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | humidity | +| **Mappings:** | | MIXS:0000100 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per cubic meter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='25 gram per cubic meter', description=None) | + diff --git a/mixs6/humidity_regm.md b/mixs6/humidity_regm.md new file mode 100644 index 00000000..30015aa4 --- /dev/null +++ b/mixs6/humidity_regm.md @@ -0,0 +1,48 @@ + +# Slot: humidity_regm + + +Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:humidity_regm](https://w3id.org/mixs/vocab/humidity_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | humidity regimen | +| **Mappings:** | | MIXS:0000568 | +| **Comments:** | | Expected value: humidity value;treatment interval and duration | +| | | Preferred unit: gram per cubic meter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/hysterectomy.md b/mixs6/hysterectomy.md new file mode 100644 index 00000000..470c3841 --- /dev/null +++ b/mixs6/hysterectomy.md @@ -0,0 +1,47 @@ + +# Slot: hysterectomy + + +Specification of whether hysterectomy was performed + +URI: [mixs.vocab:hysterectomy](https://w3id.org/mixs/vocab/hysterectomy) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hysterectomy | +| **Mappings:** | | MIXS:0000287 | +| **Comments:** | | Expected value: hysterectomy status | +| | | Occurrence: 1 | +| | | Position: 8.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='no', description=None) | + diff --git a/mixs6/ihmc_ethnicity.md b/mixs6/ihmc_ethnicity.md new file mode 100644 index 00000000..844a7619 --- /dev/null +++ b/mixs6/ihmc_ethnicity.md @@ -0,0 +1,95 @@ + +# Slot: ihmc_ethnicity + + +Ethnicity of the subject + +URI: [mixs.vocab:ihmc_ethnicity](https://w3id.org/mixs/vocab/ihmc_ethnicity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | IHMC ethnicity | +| **Mappings:** | | MIXS:0000895 | +| **Comments:** | | Expected value: IHMC code or free text | +| | | Occurrence: 1 | +| | | Position: 23.0 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='caucasian', description=None) | + diff --git a/mixs6/ihmc_medication_code.md b/mixs6/ihmc_medication_code.md new file mode 100644 index 00000000..7b541595 --- /dev/null +++ b/mixs6/ihmc_medication_code.md @@ -0,0 +1,95 @@ + +# Slot: ihmc_medication_code + + +Can include multiple medication codes + +URI: [mixs.vocab:ihmc_medication_code](https://w3id.org/mixs/vocab/ihmc_medication_code) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | IHMC medication code | +| **Mappings:** | | MIXS:0000884 | +| **Comments:** | | Expected value: IHMC code | +| | | Occurrence: m | +| | | Position: 5.0 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='810', description=None) | + diff --git a/mixs6/index.md b/mixs6/index.md new file mode 100644 index 00000000..14ad1538 --- /dev/null +++ b/mixs6/index.md @@ -0,0 +1,1562 @@ + +# Mixs schema + + +Minimal Information about any Sequence Standard + + +### Classes + + * [Air](Air.md) - air + * [AirME](AirME.md) - Combinatorial checklist Metagenome or Environmental with environmental package air + * [AirMIGSBacteria](AirMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [AirMIGSEukaryote](AirMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package air + * [AirMIGSOrg](AirMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package air + * [AirMIGSPlant](AirMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package air + * [AirMIGSVirus](AirMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [AirMIMAG](AirMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package air + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package air + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package air + * [AirMISAG](AirMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package air + * [AirMIUVIG](AirMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package air + * [BuiltEnvironment](BuiltEnvironment.md) - built environment + * [BuiltEnvironmentME](BuiltEnvironmentME.md) - Combinatorial checklist Metagenome or Environmental with environmental package built environment + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package built environment + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package built environment + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package built environment + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package built environment + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package built environment + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package built environment + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package built environment + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package built environment + * [Core](Core.md) - Core package. Do not use this directly, this is used to build other packages + * [Host-associated](Host-associated.md) - host-associated + * [Host-associatedME](Host-associatedME.md) - Combinatorial checklist Metagenome or Environmental with environmental package host-associated + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package host-associated + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package host-associated + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package host-associated + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Host-associatedMIMAG](Host-associatedMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package host-associated + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package host-associated + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package host-associated + * [Host-associatedMISAG](Host-associatedMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package host-associated + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package host-associated + * [Human-associated](Human-associated.md) - human-associated + * [Human-associatedME](Human-associatedME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-associated + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-associated + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-associated + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-associated + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-associatedMIMAG](Human-associatedMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-associated + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-associated + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-associated + * [Human-associatedMISAG](Human-associatedMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-associated + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-associated + * [Human-gut](Human-gut.md) - human-gut + * [Human-gutME](Human-gutME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-gut + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-gut + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-gut + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-gut + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-gutMIMAG](Human-gutMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-gut + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-gut + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-gut + * [Human-gutMISAG](Human-gutMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-gut + * [Human-gutMIUVIG](Human-gutMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-gut + * [Human-oral](Human-oral.md) - human-oral + * [Human-oralME](Human-oralME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-oral + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-oral + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-oral + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-oral + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-oralMIMAG](Human-oralMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-oral + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-oral + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-oral + * [Human-oralMISAG](Human-oralMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-oral + * [Human-oralMIUVIG](Human-oralMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-oral + * [Human-skin](Human-skin.md) - human-skin + * [Human-skinME](Human-skinME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-skin + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-skin + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-skin + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-skin + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-skinMIMAG](Human-skinMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-skin + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-skin + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-skin + * [Human-skinMISAG](Human-skinMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-skin + * [Human-skinMIUVIG](Human-skinMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-skin + * [Human-vaginal](Human-vaginal.md) - human-vaginal + * [Human-vaginalME](Human-vaginalME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-vaginal + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-vaginal + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-vaginal + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-vaginal + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-vaginal + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-vaginal + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-vaginal + * [Human-vaginalMISAG](Human-vaginalMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-vaginal + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-vaginal + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) - Combinatorial checklist Metagenome or Environmental with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) - Combinatorial checklist Metagenome or Environmental with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment + * [Plant-associated](Plant-associated.md) - plant-associated + * [Plant-associatedME](Plant-associatedME.md) - Combinatorial checklist Metagenome or Environmental with environmental package plant-associated + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package plant-associated + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package plant-associated + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package plant-associated + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package plant-associated + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package plant-associated + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package plant-associated + * [Plant-associatedMISAG](Plant-associatedMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package plant-associated + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package plant-associated + * [QuantityValue](QuantityValue.md) - used to record a measurement + * [Sediment](Sediment.md) - sediment + * [SedimentME](SedimentME.md) - Combinatorial checklist Metagenome or Environmental with environmental package sediment + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package sediment + * [SedimentMIGSOrg](SedimentMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package sediment + * [SedimentMIGSPlant](SedimentMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package sediment + * [SedimentMIGSVirus](SedimentMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SedimentMIMAG](SedimentMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package sediment + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package sediment + * [SedimentMISAG](SedimentMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package sediment + * [SedimentMIUVIG](SedimentMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package sediment + * [Soil](Soil.md) - soil + * [SoilME](SoilME.md) - Combinatorial checklist Metagenome or Environmental with environmental package soil + * [SoilMIGSBacteria](SoilMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package soil + * [SoilMIGSOrg](SoilMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package soil + * [SoilMIGSPlant](SoilMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package soil + * [SoilMIGSVirus](SoilMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [SoilMIMAG](SoilMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package soil + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil + * [SoilMISAG](SoilMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package soil + * [SoilMIUVIG](SoilMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package soil + * [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + * [WastewaterSludgeME](WastewaterSludgeME.md) - Combinatorial checklist Metagenome or Environmental with environmental package wastewater_sludge + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package wastewater_sludge + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package wastewater_sludge + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package wastewater_sludge + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package wastewater_sludge + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package wastewater_sludge + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package wastewater_sludge + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package wastewater_sludge + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package wastewater_sludge + * [Water](Water.md) - water + * [WaterME](WaterME.md) - Combinatorial checklist Metagenome or Environmental with environmental package water + * [WaterMIGSBacteria](WaterMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package water + * [WaterMIGSOrg](WaterMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package water + * [WaterMIGSPlant](WaterMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package water + * [WaterMIGSVirus](WaterMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + * [WaterMIMAG](WaterMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package water + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package water + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package water + * [WaterMISAG](WaterMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package water + * [WaterMIUVIG](WaterMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package water + +### Mixins + + * [ME](ME.md) - Metagenome or Environmental + * [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + * [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + * [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + * [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + * [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + * [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + * [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + * [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + * [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + * [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome + +### Slots + + * [core field](core_field.md) - basic fields + * [environment field](environment_field.md) - field describing environmental aspect of a sample + * [abs_air_humidity](abs_air_humidity.md) - Actual mass of water vapor - mh20 - present in the air water vapor mixture + * [add_recov_method](add_recov_method.md) - Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * [additional_info](additional_info.md) - Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * [address](address.md) - The street name and building number where the sampling occurred. + * [adj_room](adj_room.md) - List of rooms (room number, room name) immediately adjacent to the sampling room + * [aero_struc](aero_struc.md) - Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * [agrochem_addition](agrochem_addition.md) - Addition of fertilizers, pesticides, etc. - amount and time of applications + * [air_temp](air_temp.md) - Temperature of the air at the time of sampling + * [air_temp_regm](air_temp_regm.md) - Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * [al_sat](al_sat.md) - Aluminum saturation (esp. For tropical soils) + * [al_sat_meth](al_sat_meth.md) - Reference or method used in determining Al saturation + * [alkalinity](alkalinity.md) - Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * [alkalinity_method](alkalinity_method.md) - Method used for alkalinity measurement + * [alkyl_diethers](alkyl_diethers.md) - Concentration of alkyl diethers + * [alt](alt.md) - Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * [aminopept_act](aminopept_act.md) - Measurement of aminopeptidase activity + * [ammonium](ammonium.md) - Concentration of ammonium in the sample + * [amniotic_fluid_color](amniotic_fluid_color.md) - Specification of the color of the amniotic fluid sample + * [amount_light](amount_light.md) - The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * [ances_data](ances_data.md) - Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * [annual_precpt](annual_precpt.md) - The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * [annual_temp](annual_temp.md) - Mean annual temperature + * [antibiotic_regm](antibiotic_regm.md) - Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * [api](api.md) - API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * [arch_struc](arch_struc.md) - An architectural structure is a human-made, free-standing, immobile outdoor construction + * [aromatics_pc](aromatics_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [asphaltenes_pc](asphaltenes_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [atmospheric_data](atmospheric_data.md) - Measurement of atmospheric data; can include multiple data + * [avg_dew_point](avg_dew_point.md) - The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * [avg_occup](avg_occup.md) - Daily average occupancy of room + * [avg_temp](avg_temp.md) - The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * [bac_prod](bac_prod.md) - Bacterial production in the water column measured by isotope uptake + * [bac_resp](bac_resp.md) - Measurement of bacterial respiration in the water column + * [bacteria_carb_prod](bacteria_carb_prod.md) - Measurement of bacterial carbon production + * [barometric_press](barometric_press.md) - Force per unit area exerted against a surface by the weight of air above that surface + * [basin](basin.md) - Name of the basin (e.g. Campos) + * [bathroom_count](bathroom_count.md) - The number of bathrooms in the building + * [bedroom_count](bedroom_count.md) - The number of bedrooms in the building + * [benzene](benzene.md) - Concentration of benzene in the sample + * [biochem_oxygen_dem](biochem_oxygen_dem.md) - Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * [biocide](biocide.md) - List of biocides (commercial name of product and supplier) and date of administration + * [biocide_admin_method](biocide_admin_method.md) - Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * [biol_stat](biol_stat.md) - The level of genome modification. + * [biomass](biomass.md) - Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * [biotic_regm](biotic_regm.md) - Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * [birth_control](birth_control.md) - Specification of birth control medication used + * [bishomohopanol](bishomohopanol.md) - Concentration of bishomohopanol + * [blood_blood_disord](blood_blood_disord.md) - History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * [bromide](bromide.md) - Concentration of bromide + * [build_docs](build_docs.md) - The building design, construction and operation documents + * [build_occup_type](build_occup_type.md) - The primary function for which a building or discrete part of a building is intended to be used + * [building_setting](building_setting.md) - A location (geography) where a building is set + * [built_struc_age](built_struc_age.md) - The age of the built structure since construction + * [built_struc_set](built_struc_set.md) - The characterization of the location of the built structure as high or low human density + * [built_struc_type](built_struc_type.md) - A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * [calcium](calcium.md) - Concentration of calcium in the sample + * [carb_dioxide](carb_dioxide.md) - Carbon dioxide (gas) amount or concentration at the time of sampling + * [carb_monoxide](carb_monoxide.md) - Carbon monoxide (gas) amount or concentration at the time of sampling + * [carb_nitro_ratio](carb_nitro_ratio.md) - Ratio of amount or concentrations of carbon to nitrogen + * [ceil_area](ceil_area.md) - The area of the ceiling space within the room + * [ceil_cond](ceil_cond.md) - The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * [ceil_finish_mat](ceil_finish_mat.md) - The type of material used to finish a ceiling + * [ceil_struc](ceil_struc.md) - The construction format of the ceiling + * [ceil_texture](ceil_texture.md) - The feel, appearance, or consistency of a ceiling surface + * [ceil_thermal_mass](ceil_thermal_mass.md) - The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * [ceil_type](ceil_type.md) - The type of ceiling according to the ceiling's appearance or construction + * [ceil_water_mold](ceil_water_mold.md) - Signs of the presence of mold or mildew on the ceiling + * [chem_administration](chem_administration.md) - List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * [chem_mutagen](chem_mutagen.md) - Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * [chem_oxygen_dem](chem_oxygen_dem.md) - A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * [chem_treatment](chem_treatment.md) - List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * [chem_treatment_method](chem_treatment_method.md) - Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * [chloride](chloride.md) - Concentration of chloride in the sample + * [chlorophyll](chlorophyll.md) - Concentration of chlorophyll + * [climate_environment](climate_environment.md) - Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * [collection_date](collection_date.md) - The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * [ME➞collection_date](ME_collection_date.md) + * [MIGS bacteria➞collection_date](MIGS_bacteria_collection_date.md) + * [MIGS eukaryote➞collection_date](MIGS_eukaryote_collection_date.md) + * [MIGS org➞collection_date](MIGS_org_collection_date.md) + * [MIGS plant➞collection_date](MIGS_plant_collection_date.md) + * [MIGS virus➞collection_date](MIGS_virus_collection_date.md) + * [MIMAG➞collection_date](MIMAG_collection_date.md) + * [MIMARKS specimen➞collection_date](MIMARKS_specimen_collection_date.md) + * [MIMARKS survey➞collection_date](MIMARKS_survey_collection_date.md) + * [MISAG➞collection_date](MISAG_collection_date.md) + * [MIUVIG➞collection_date](MIUVIG_collection_date.md) + * [conduc](conduc.md) - Electrical conductivity of water + * [cool_syst_id](cool_syst_id.md) - The cooling system identifier + * [crop_rotation](crop_rotation.md) - Whether or not crop is rotated, and if yes, rotation schedule + * [cult_root_med](cult_root_med.md) - Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * [cur_land_use](cur_land_use.md) - Present state of sample site + * [cur_vegetation](cur_vegetation.md) - Vegetation classification from one or more standard classification systems, or agricultural crop + * [cur_vegetation_meth](cur_vegetation_meth.md) - Reference or method used in vegetation classification + * [date_last_rain](date_last_rain.md) - The date of the last time it rained + * [density](density.md) - Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * [depos_env](depos_env.md) - Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * [depth](depth.md) - The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + * [dermatology_disord](dermatology_disord.md) - History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * [dew_point](dew_point.md) - The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * [diet_last_six_month](diet_last_six_month.md) - Specification of major diet changes in the last six months, if yes the change should be specified + * [diether_lipids](diether_lipids.md) - Concentration of diether lipids; can include multiple types of diether lipids + * [diss_carb_dioxide](diss_carb_dioxide.md) - Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * [diss_hydrogen](diss_hydrogen.md) - Concentration of dissolved hydrogen + * [diss_inorg_carb](diss_inorg_carb.md) - Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * [diss_inorg_nitro](diss_inorg_nitro.md) - Concentration of dissolved inorganic nitrogen + * [diss_inorg_phosp](diss_inorg_phosp.md) - Concentration of dissolved inorganic phosphorus in the sample + * [diss_iron](diss_iron.md) - Concentration of dissolved iron in the sample + * [diss_org_carb](diss_org_carb.md) - Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * [diss_org_nitro](diss_org_nitro.md) - Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * [diss_oxygen](diss_oxygen.md) - Concentration of dissolved oxygen + * [diss_oxygen_fluid](diss_oxygen_fluid.md) - Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * [dominant_hand](dominant_hand.md) - Dominant hand of the subject + * [door_comp_type](door_comp_type.md) - The composite type of the door + * [door_cond](door_cond.md) - The phsical condition of the door + * [door_direct](door_direct.md) - The direction the door opens + * [door_loc](door_loc.md) - The relative location of the door in the room + * [door_mat](door_mat.md) - The material the door is composed of + * [door_move](door_move.md) - The type of movement of the door + * [door_size](door_size.md) - The size of the door + * [door_type](door_type.md) - The type of door material + * [door_type_metal](door_type_metal.md) - The type of metal door + * [door_type_wood](door_type_wood.md) - The type of wood door + * [door_water_mold](door_water_mold.md) - Signs of the presence of mold or mildew on a door + * [douche](douche.md) - Date of most recent douche + * [down_par](down_par.md) - Visible waveband radiance and irradiance measurements in the water column + * [drainage_class](drainage_class.md) - Drainage classification from a standard system such as the USDA system + * [drawings](drawings.md) - The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * [drug_usage](drug_usage.md) - Any drug used by subject and the frequency of usage; can include multiple drugs used + * [efficiency_percent](efficiency_percent.md) - Percentage of volatile solids removed from the anaerobic digestor + * [elev](elev.md) - Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * [elevator](elevator.md) - The number of elevators within the built structure + * [emulsions](emulsions.md) - Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * [env_broad_scale](env_broad_scale.md) - In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [ME➞env_broad_scale](ME_env_broad_scale.md) + * [MIGS bacteria➞env_broad_scale](MIGS_bacteria_env_broad_scale.md) + * [MIGS eukaryote➞env_broad_scale](MIGS_eukaryote_env_broad_scale.md) + * [MIGS org➞env_broad_scale](MIGS_org_env_broad_scale.md) + * [MIGS plant➞env_broad_scale](MIGS_plant_env_broad_scale.md) + * [MIGS virus➞env_broad_scale](MIGS_virus_env_broad_scale.md) + * [MIMAG➞env_broad_scale](MIMAG_env_broad_scale.md) + * [MIMARKS specimen➞env_broad_scale](MIMARKS_specimen_env_broad_scale.md) + * [MIMARKS survey➞env_broad_scale](MIMARKS_survey_env_broad_scale.md) + * [MISAG➞env_broad_scale](MISAG_env_broad_scale.md) + * [MIUVIG➞env_broad_scale](MIUVIG_env_broad_scale.md) + * [env_local_scale](env_local_scale.md) - In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [ME➞env_local_scale](ME_env_local_scale.md) + * [MIGS bacteria➞env_local_scale](MIGS_bacteria_env_local_scale.md) + * [MIGS eukaryote➞env_local_scale](MIGS_eukaryote_env_local_scale.md) + * [MIGS org➞env_local_scale](MIGS_org_env_local_scale.md) + * [MIGS plant➞env_local_scale](MIGS_plant_env_local_scale.md) + * [MIGS virus➞env_local_scale](MIGS_virus_env_local_scale.md) + * [MIMAG➞env_local_scale](MIMAG_env_local_scale.md) + * [MIMARKS specimen➞env_local_scale](MIMARKS_specimen_env_local_scale.md) + * [MIMARKS survey➞env_local_scale](MIMARKS_survey_env_local_scale.md) + * [MISAG➞env_local_scale](MISAG_env_local_scale.md) + * [MIUVIG➞env_local_scale](MIUVIG_env_local_scale.md) + * [env_medium](env_medium.md) - In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [ME➞env_medium](ME_env_medium.md) + * [MIGS bacteria➞env_medium](MIGS_bacteria_env_medium.md) + * [MIGS eukaryote➞env_medium](MIGS_eukaryote_env_medium.md) + * [MIGS org➞env_medium](MIGS_org_env_medium.md) + * [MIGS plant➞env_medium](MIGS_plant_env_medium.md) + * [MIGS virus➞env_medium](MIGS_virus_env_medium.md) + * [MIMAG➞env_medium](MIMAG_env_medium.md) + * [MIMARKS specimen➞env_medium](MIMARKS_specimen_env_medium.md) + * [MIMARKS survey➞env_medium](MIMARKS_survey_env_medium.md) + * [MISAG➞env_medium](MISAG_env_medium.md) + * [MIUVIG➞env_medium](MIUVIG_env_medium.md) + * [escalator](escalator.md) - The number of escalators within the built structure + * [ethylbenzene](ethylbenzene.md) - Concentration of ethylbenzene in the sample + * [exp_duct](exp_duct.md) - The amount of exposed ductwork in the room + * [exp_pipe](exp_pipe.md) - The number of exposed pipes in the room + * [ext_door](ext_door.md) - The number of exterior doors in the built structure + * [ext_wall_orient](ext_wall_orient.md) - The orientation of the exterior wall + * [ext_window_orient](ext_window_orient.md) - The compass direction the exterior window of the room is facing + * [extreme_event](extreme_event.md) - Unusual physical events that may have affected microbial populations + * [extreme_salinity](extreme_salinity.md) - Measured salinity + * [fao_class](fao_class.md) - Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * [fertilizer_regm](fertilizer_regm.md) - Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * [field](field.md) - Name of the hydrocarbon field (e.g. Albacora) + * [filter_type](filter_type.md) - A device which removes solid particulates or airborne molecular contaminants + * [fire](fire.md) - Historical and/or physical evidence of fire + * [fireplace_type](fireplace_type.md) - A firebox with chimney + * [flooding](flooding.md) - Historical and/or physical evidence of flooding + * [floor_age](floor_age.md) - The time period since installment of the carpet or flooring + * [floor_area](floor_area.md) - The area of the floor space within the room + * [floor_cond](floor_cond.md) - The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * [floor_count](floor_count.md) - The number of floors in the building, including basements and mechanical penthouse + * [floor_finish_mat](floor_finish_mat.md) - The floor covering type; the finished surface that is walked on + * [floor_struc](floor_struc.md) - Refers to the structural elements and subfloor upon which the finish flooring is installed + * [floor_thermal_mass](floor_thermal_mass.md) - The ability of the floor to provide inertia against temperature fluctuations + * [floor_water_mold](floor_water_mold.md) - Signs of the presence of mold or mildew in a room + * [fluor](fluor.md) - Raw or converted fluorescence of water + * [foetal_health_stat](foetal_health_stat.md) - Specification of foetal health status, should also include abortion + * [freq_clean](freq_clean.md) - The number of times the building is cleaned per week + * [freq_cook](freq_cook.md) - The number of times a meal is cooked per week + * [fungicide_regm](fungicide_regm.md) - Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * [furniture](furniture.md) - The types of furniture present in the sampled room + * [gaseous_environment](gaseous_environment.md) - Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * [gaseous_substances](gaseous_substances.md) - Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * [gastrointest_disord](gastrointest_disord.md) - History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * [gender_restroom](gender_restroom.md) - The gender type of the restroom + * [genetic_mod](genetic_mod.md) - Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * [geo_loc_name](geo_loc_name.md) - The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * [ME➞geo_loc_name](ME_geo_loc_name.md) + * [MIGS bacteria➞geo_loc_name](MIGS_bacteria_geo_loc_name.md) + * [MIGS eukaryote➞geo_loc_name](MIGS_eukaryote_geo_loc_name.md) + * [MIGS org➞geo_loc_name](MIGS_org_geo_loc_name.md) + * [MIGS plant➞geo_loc_name](MIGS_plant_geo_loc_name.md) + * [MIGS virus➞geo_loc_name](MIGS_virus_geo_loc_name.md) + * [MIMAG➞geo_loc_name](MIMAG_geo_loc_name.md) + * [MIMARKS specimen➞geo_loc_name](MIMARKS_specimen_geo_loc_name.md) + * [MIMARKS survey➞geo_loc_name](MIMARKS_survey_geo_loc_name.md) + * [MISAG➞geo_loc_name](MISAG_geo_loc_name.md) + * [MIUVIG➞geo_loc_name](MIUVIG_geo_loc_name.md) + * [gestation_state](gestation_state.md) - Specification of the gestation state + * [glucosidase_act](glucosidase_act.md) - Measurement of glucosidase activity + * [gravidity](gravidity.md) - Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * [gravity](gravity.md) - Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * [growth_facil](growth_facil.md) - Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * [growth_habit](growth_habit.md) - Characteristic shape, appearance or growth form of a plant species + * [growth_hormone_regm](growth_hormone_regm.md) - Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * [gynecologic_disord](gynecologic_disord.md) - History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * [hall_count](hall_count.md) - The total count of hallways and cooridors in the built structure + * [handidness](handidness.md) - The handidness of the individual sampled + * [hc_produced](hc_produced.md) - Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * [hcr](hcr.md) - Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * [hcr_fw_salinity](hcr_fw_salinity.md) - Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * [hcr_geol_age](hcr_geol_age.md) - Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * [hcr_pressure](hcr_pressure.md) - Original pressure of the hydrocarbon resource + * [hcr_temp](hcr_temp.md) - Original temperature of the hydrocarbon resource + * [heat_cool_type](heat_cool_type.md) - Methods of conditioning or heating a room or building + * [heat_deliv_loc](heat_deliv_loc.md) - The location of heat delivery within the room + * [heat_system_deliv_meth](heat_system_deliv_meth.md) - The method by which the heat is delivered through the system + * [heat_system_id](heat_system_id.md) - The heating system identifier + * [heavy_metals](heavy_metals.md) - Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * [heavy_metals_meth](heavy_metals_meth.md) - Reference or method used in determining heavy metals + * [height_carper_fiber](height_carper_fiber.md) - The average carpet fiber height in the indoor environment + * [herbicide_regm](herbicide_regm.md) - Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [horizon](horizon.md) - Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * [horizon_meth](horizon_meth.md) - Reference or method used in determining the horizon + * [host_age](host_age.md) - Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * [host_blood_press_diast](host_blood_press_diast.md) - Resting diastolic blood pressure, measured as mm mercury + * [host_blood_press_syst](host_blood_press_syst.md) - Resting systolic blood pressure, measured as mm mercury + * [host_body_habitat](host_body_habitat.md) - Original body habitat where the sample was obtained from + * [host_body_mass_index](host_body_mass_index.md) - Body mass index, calculated as weight/(height)squared + * [host_body_product](host_body_product.md) - Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * [host_body_site](host_body_site.md) - Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * [host_body_temp](host_body_temp.md) - Core body temperature of the host when sample was collected + * [host_color](host_color.md) - The color of host + * [host_common_name](host_common_name.md) - Common name of the host, e.g. Human + * [host_diet](host_diet.md) - Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * [host_disease_stat](host_disease_stat.md) - List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * [host_dry_mass](host_dry_mass.md) - Measurement of dry mass + * [host_family_relationship](host_family_relationship.md) - Relationships to other hosts in the same study; can include multiple relationships + * [host_genotype](host_genotype.md) - Observed genotype + * [host_growth_cond](host_growth_cond.md) - Literature reference giving growth conditions of the host + * [host_height](host_height.md) - The height of subject + * [host_hiv_stat](host_hiv_stat.md) - HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * [host_infra_specific_name](host_infra_specific_name.md) - Taxonomic information about the host below subspecies level + * [host_infra_specific_rank](host_infra_specific_rank.md) - Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * [host_last_meal](host_last_meal.md) - Content of last meal and time since feeding; can include multiple values + * [host_length](host_length.md) - The length of subject + * [host_life_stage](host_life_stage.md) - Description of life stage of host + * [host_occupation](host_occupation.md) - Most frequent job performed by subject + * [host_phenotype](host_phenotype.md) - Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * [host_pulse](host_pulse.md) - Resting pulse, measured as beats per minute + * [host_sex](host_sex.md) - Physical sex of the host + * [host_shape](host_shape.md) - Morphological shape of host + * [host_subject_id](host_subject_id.md) - A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * [host_substrate](host_substrate.md) - The growth substrate of the host + * [host_symbiont](host_symbiont.md) - The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * [host_taxid](host_taxid.md) - NCBI taxon id of the host, e.g. 9606 + * [host_tot_mass](host_tot_mass.md) - Total mass of the host at collection, the unit depends on host + * [host_wet_mass](host_wet_mass.md) - Measurement of wet mass + * [hrt](hrt.md) - Whether subject had hormone replacement theraphy, and if yes start date + * [humidity](humidity.md) - Amount of water vapour in the air, at the time of sampling + * [humidity_regm](humidity_regm.md) - Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [hysterectomy](hysterectomy.md) - Specification of whether hysterectomy was performed + * [ihmc_ethnicity](ihmc_ethnicity.md) - Ethnicity of the subject + * [ihmc_medication_code](ihmc_medication_code.md) - Can include multiple medication codes + * [indoor_space](indoor_space.md) - A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * [indoor_surf](indoor_surf.md) - Type of indoor surface + * [indust_eff_percent](indust_eff_percent.md) - Percentage of industrial effluents received by wastewater treatment plant + * [inorg_particles](inorg_particles.md) - Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * [inside_lux](inside_lux.md) - The recorded value at sampling time (power density) + * [int_wall_cond](int_wall_cond.md) - The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * [iw_bt_date_well](iw_bt_date_well.md) - Injection water breakthrough date per well following a secondary and/or tertiary recovery + * [iwf](iwf.md) - Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * [kidney_disord](kidney_disord.md) - History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * [last_clean](last_clean.md) - The last time the floor was cleaned (swept, mopped, vacuumed) + * [lat_lon](lat_lon.md) - The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * [ME➞lat_lon](ME_lat_lon.md) + * [MIGS bacteria➞lat_lon](MIGS_bacteria_lat_lon.md) + * [MIGS eukaryote➞lat_lon](MIGS_eukaryote_lat_lon.md) + * [MIGS org➞lat_lon](MIGS_org_lat_lon.md) + * [MIGS plant➞lat_lon](MIGS_plant_lat_lon.md) + * [MIGS virus➞lat_lon](MIGS_virus_lat_lon.md) + * [MIMAG➞lat_lon](MIMAG_lat_lon.md) + * [MIMARKS specimen➞lat_lon](MIMARKS_specimen_lat_lon.md) + * [MIMARKS survey➞lat_lon](MIMARKS_survey_lat_lon.md) + * [MISAG➞lat_lon](MISAG_lat_lon.md) + * [MIUVIG➞lat_lon](MIUVIG_lat_lon.md) + * [light_intensity](light_intensity.md) - Measurement of light intensity + * [light_regm](light_regm.md) - Information about treatment(s) involving exposure to light, including both light intensity and quality. + * [light_type](light_type.md) - Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * [link_addit_analys](link_addit_analys.md) - Link to additional analysis results performed on the sample + * [link_class_info](link_class_info.md) - Link to digitized soil maps or other soil classification information + * [link_climate_info](link_climate_info.md) - Link to climate resource + * [lithology](lithology.md) - Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * [liver_disord](liver_disord.md) - History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * [local_class](local_class.md) - Soil classification based on local soil classification system + * [local_class_meth](local_class_meth.md) - Reference or method used in determining the local soil classification + * [magnesium](magnesium.md) - Concentration of magnesium in the sample + * [maternal_health_stat](maternal_health_stat.md) - Specification of the maternal health status + * [max_occup](max_occup.md) - The maximum amount of people allowed in the indoor environment + * [mean_frict_vel](mean_frict_vel.md) - Measurement of mean friction velocity + * [mean_peak_frict_vel](mean_peak_frict_vel.md) - Measurement of mean peak friction velocity + * [mech_struc](mech_struc.md) - mechanical structure: a moving structure + * [mechanical_damage](mechanical_damage.md) - Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * [medic_hist_perform](medic_hist_perform.md) - Whether full medical history was collected + * [menarche](menarche.md) - Date of most recent menstruation + * [menopause](menopause.md) - Date of onset of menopause + * [methane](methane.md) - Methane (gas) amount or concentration at the time of sampling + * [microbial_biomass](microbial_biomass.md) - The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * [microbial_biomass_meth](microbial_biomass_meth.md) - Reference or method used in determining microbial biomass + * [mineral_nutr_regm](mineral_nutr_regm.md) - Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * [misc_param](misc_param.md) - Any other measurement performed or parameter collected, that is not listed here + * [n_alkanes](n_alkanes.md) - Concentration of n-alkanes; can include multiple n-alkanes + * [nitrate](nitrate.md) - Concentration of nitrate in the sample + * [nitrite](nitrite.md) - Concentration of nitrite in the sample + * [nitro](nitro.md) - Concentration of nitrogen (total) + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) - Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) - History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * [nose_throat_disord](nose_throat_disord.md) - History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * [number_pets](number_pets.md) - The number of pets residing in the sampled space + * [number_plants](number_plants.md) - The number of plant(s) in the sampling space + * [number_resident](number_resident.md) - The number of individuals currently occupying in the sampling location + * [occup_density_samp](occup_density_samp.md) - Average number of occupants at time of sampling per square footage + * [occup_document](occup_document.md) - The type of documentation of occupancy + * [occup_samp](occup_samp.md) - Number of occupants present at time of sample within the given space + * [org_carb](org_carb.md) - Concentration of organic carbon + * [org_matter](org_matter.md) - Concentration of organic matter + * [org_nitro](org_nitro.md) - Concentration of organic nitrogen + * [org_particles](org_particles.md) - Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * [organism_count](organism_count.md) - Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * [organism_count_qpcr_info](organism_count_qpcr_info.md) - If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * [owc_tvdss](owc_tvdss.md) - Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * [oxy_stat_samp](oxy_stat_samp.md) - Oxygenation status of sample + * [oxygen](oxygen.md) - Oxygen (gas) amount or concentration at the time of sampling + * [part_org_carb](part_org_carb.md) - Concentration of particulate organic carbon + * [part_org_nitro](part_org_nitro.md) - Concentration of particulate organic nitrogen + * [particle_class](particle_class.md) - Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * [permeability](permeability.md) - Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * [perturbation](perturbation.md) - Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * [pesticide_regm](pesticide_regm.md) - Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * [pet_farm_animal](pet_farm_animal.md) - Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * [petroleum_hydrocarb](petroleum_hydrocarb.md) - Concentration of petroleum hydrocarbon + * [ph](ph.md) - Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * [ph_meth](ph_meth.md) - Reference or method used in determining ph + * [ph_regm](ph_regm.md) - Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * [phaeopigments](phaeopigments.md) - Concentration of phaeopigments; can include multiple phaeopigments + * [phosphate](phosphate.md) - Concentration of phosphate + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) - Concentration of phospholipid fatty acids; can include multiple values + * [photon_flux](photon_flux.md) - Measurement of photon flux + * [plant_growth_med](plant_growth_med.md) - Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * [plant_product](plant_product.md) - Substance produced by the plant, where the sample was obtained from + * [plant_sex](plant_sex.md) - Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * [plant_struc](plant_struc.md) - Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * [pollutants](pollutants.md) - Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * [pool_dna_extracts](pool_dna_extracts.md) - Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * [porosity](porosity.md) - Porosity of deposited sediment is volume of voids divided by the total volume of sample + * [potassium](potassium.md) - Concentration of potassium in the sample + * [pour_point](pour_point.md) - Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * [pre_treatment](pre_treatment.md) - The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * [pregnancy](pregnancy.md) - Date due of pregnancy + * [pres_animal](pres_animal.md) - The number and type of animals present in the sampling space + * [pressure](pressure.md) - Pressure to which the sample is subject to, in atmospheres + * [previous_land_use](previous_land_use.md) - Previous land use and dates + * [previous_land_use_meth](previous_land_use_meth.md) - Reference or method used in determining previous land use and dates + * [primary_prod](primary_prod.md) - Measurement of primary production, generally measured as isotope uptake + * [primary_treatment](primary_treatment.md) - The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * [prod_rate](prod_rate.md) - Oil and/or gas production rates per well (e.g. 524 m3 / day) + * [prod_start_date](prod_start_date.md) - Date of field's first production + * [profile_position](profile_position.md) - Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * [pulmonary_disord](pulmonary_disord.md) - History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * [quad_pos](quad_pos.md) - The quadrant position of the sampling room within the building + * [radiation_regm](radiation_regm.md) - Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * [rainfall_regm](rainfall_regm.md) - Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [reactor_type](reactor_type.md) - Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * [redox_potential](redox_potential.md) - Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * [rel_air_humidity](rel_air_humidity.md) - Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * [rel_humidity_out](rel_humidity_out.md) - The recorded outside relative humidity value at the time of sampling + * [rel_samp_loc](rel_samp_loc.md) - The sampling location within the train car + * [reservoir](reservoir.md) - Name of the reservoir (e.g. Carapebus) + * [resins_pc](resins_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [resp_part_matter](resp_part_matter.md) - Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * [room_air_exch_rate](room_air_exch_rate.md) - The rate at which outside air replaces indoor air in a given space + * [room_architec_element](room_architec_element.md) - The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * [room_condt](room_condt.md) - The condition of the room at the time of sampling + * [room_connected](room_connected.md) - List of rooms connected to the sampling room by a doorway + * [room_count](room_count.md) - The total count of rooms in the built structure including all room types + * [room_dim](room_dim.md) - The length, width and height of sampling room + * [room_door_dist](room_door_dist.md) - Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * [room_door_share](room_door_share.md) - List of room(s) (room number, room name) sharing a door with the sampling room + * [room_hallway](room_hallway.md) - List of room(s) (room number, room name) located in the same hallway as sampling room + * [room_loc](room_loc.md) - The position of the room within the building + * [room_moist_damage_hist](room_moist_damage_hist.md) - The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * [room_net_area](room_net_area.md) - The net floor area of sampling room. Net area excludes wall thicknesses + * [room_occup](room_occup.md) - Count of room occupancy at time of sampling + * [room_samp_pos](room_samp_pos.md) - The horizontal sampling position in the room relative to architectural elements + * [room_type](room_type.md) - The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * [room_vol](room_vol.md) - Volume of sampling room + * [room_wall_share](room_wall_share.md) - List of room(s) (room number, room name) sharing a wall with the sampling room + * [room_window_count](room_window_count.md) - Number of windows in the room + * [root_cond](root_cond.md) - Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * [root_med_carbon](root_med_carbon.md) - Source of organic carbon in the culture rooting medium; e.g. sucrose. + * [root_med_macronutr](root_med_macronutr.md) - Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * [root_med_micronutr](root_med_micronutr.md) - Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * [root_med_ph](root_med_ph.md) - pH measurement of the culture rooting medium; e.g. 5.5. + * [root_med_regl](root_med_regl.md) - Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * [root_med_solid](root_med_solid.md) - Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * [root_med_suppl](root_med_suppl.md) - Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * [salinity](salinity.md) - Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * [salinity_meth](salinity_meth.md) - Reference or method used in determining salinity + * [salt_regm](salt_regm.md) - Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * [samp_capt_status](samp_capt_status.md) - Reason for the sample + * [samp_collection_point](samp_collection_point.md) - Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * [samp_dis_stage](samp_dis_stage.md) - Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * [samp_floor](samp_floor.md) - The floor of the building, where the sampling room is located + * [samp_loc_corr_rate](samp_loc_corr_rate.md) - Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * [samp_md](samp_md.md) - In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * [samp_preserv](samp_preserv.md) - Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * [samp_room_id](samp_room_id.md) - Sampling room number. This ID should be consistent with the designations on the building floor plans + * [samp_salinity](samp_salinity.md) - Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * [samp_sort_meth](samp_sort_meth.md) - Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * [samp_store_dur](samp_store_dur.md) - Duration for which the sample was stored + * [samp_store_loc](samp_store_loc.md) - Location at which sample was stored, usually name of a specific freezer/room + * [samp_store_temp](samp_store_temp.md) - Temperature at which sample was stored, e.g. -80 degree Celsius + * [samp_subtype](samp_subtype.md) - Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * [samp_time_out](samp_time_out.md) - The recent and long term history of outside sampling + * [samp_transport_cond](samp_transport_cond.md) - Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * [samp_tvdss](samp_tvdss.md) - Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * [samp_type](samp_type.md) - Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) - Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * [samp_weather](samp_weather.md) - The weather on the sampling day + * [samp_well_name](samp_well_name.md) - Name of the well (e.g. BXA1123) where sample was taken + * [saturates_pc](saturates_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [season](season.md) - The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * [season_environment](season_environment.md) - Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * [season_precpt](season_precpt.md) - The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * [season_temp](season_temp.md) - Mean seasonal temperature + * [season_use](season_use.md) - The seasons the space is occupied + * [secondary_treatment](secondary_treatment.md) - The process for substantially degrading the biological content of the sewage + * [sediment_type](sediment_type.md) - Information about the sediment type based on major constituents + * [sewage_type](sewage_type.md) - Type of wastewater treatment plant as municipial or industrial + * [sexual_act](sexual_act.md) - Current sexual partner and frequency of sex + * [shading_device_cond](shading_device_cond.md) - The physical condition of the shading device at the time of sampling + * [shading_device_loc](shading_device_loc.md) - The location of the shading device in relation to the built structure + * [shading_device_mat](shading_device_mat.md) - The material the shading device is composed of + * [shading_device_type](shading_device_type.md) - The type of shading device + * [shading_device_water_mold](shading_device_water_mold.md) - Signs of the presence of mold or mildew on the shading device + * [sieving](sieving.md) - Collection design of pooled samples and/or sieve size and amount of sample sieved + * [silicate](silicate.md) - Concentration of silicate + * [size_frac_low](size_frac_low.md) - Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * [size_frac_up](size_frac_up.md) - Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * [slope_aspect](slope_aspect.md) - The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * [slope_gradient](slope_gradient.md) - Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * [sludge_retent_time](sludge_retent_time.md) - The time activated sludge remains in reactor + * [smoker](smoker.md) - Specification of smoking status + * [sodium](sodium.md) - Sodium concentration in the sample + * [soil_type](soil_type.md) - Soil series name or other lower-level classification + * [soil_type_meth](soil_type_meth.md) - Reference or method used in determining soil series name or other lower-level classification + * [solar_irradiance](solar_irradiance.md) - The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * [soluble_inorg_mat](soluble_inorg_mat.md) - Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * [soluble_org_mat](soluble_org_mat.md) - Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * [soluble_react_phosp](soluble_react_phosp.md) - Concentration of soluble reactive phosphorus + * [space_typ_state](space_typ_state.md) - Customary or normal state of the space + * [special_diet](special_diet.md) - Specification of special diet; can include multiple special diets + * [specific](specific.md) - The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * [specific_humidity](specific_humidity.md) - The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * [sr_dep_env](sr_dep_env.md) - Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * [sr_geol_age](sr_geol_age.md) - Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * [sr_kerog_type](sr_kerog_type.md) - Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * [sr_lithology](sr_lithology.md) - Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * [standing_water_regm](standing_water_regm.md) - Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [store_cond](store_cond.md) - Explain how and for how long the soil sample was stored before DNA extraction + * [study_complt_stat](study_complt_stat.md) - Specification of study completion status, if no the reason should be specified + * [substructure_type](substructure_type.md) - The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * [sulfate](sulfate.md) - Concentration of sulfate in the sample + * [sulfate_fw](sulfate_fw.md) - Original sulfate concentration in the hydrocarbon resource + * [sulfide](sulfide.md) - Concentration of sulfide in the sample + * [surf_air_cont](surf_air_cont.md) - Contaminant identified on surface + * [surf_humidity](surf_humidity.md) - Surfaces: water activity as a function of air and material moisture + * [surf_material](surf_material.md) - Surface materials at the point of sampling + * [surf_moisture](surf_moisture.md) - Water held on a surface + * [surf_moisture_ph](surf_moisture_ph.md) - ph measurement of surface + * [surf_temp](surf_temp.md) - Temperature of the surface at the time of sampling + * [suspend_part_matter](suspend_part_matter.md) - Concentration of suspended particulate matter + * [suspend_solids](suspend_solids.md) - Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * [tan](tan.md) - Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * [temp](temp.md) - Temperature of the sample at the time of sampling + * [temp_out](temp_out.md) - The recorded temperature value at sampling time outside + * [tertiary_treatment](tertiary_treatment.md) - The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * [texture](texture.md) - The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * [texture_meth](texture_meth.md) - Reference or method used in determining soil texture + * [tidal_stage](tidal_stage.md) - Stage of tide + * [tillage](tillage.md) - Note method(s) used for tilling + * [time_last_toothbrush](time_last_toothbrush.md) - Specification of the time since last toothbrushing + * [time_since_last_wash](time_since_last_wash.md) - Specification of the time since last wash + * [tiss_cult_growth_med](tiss_cult_growth_med.md) - Description of plant tissue culture growth media used + * [toluene](toluene.md) - Concentration of toluene in the sample + * [tot_carb](tot_carb.md) - Total carbon content + * [tot_depth_water_col](tot_depth_water_col.md) - Measurement of total depth of water column + * [tot_diss_nitro](tot_diss_nitro.md) - Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * [tot_inorg_nitro](tot_inorg_nitro.md) - Total inorganic nitrogen content + * [tot_iron](tot_iron.md) - Concentration of total iron in the sample + * [tot_nitro](tot_nitro.md) - Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * [tot_nitro_content](tot_nitro_content.md) - Total nitrogen content of the sample + * [tot_nitro_content_meth](tot_nitro_content_meth.md) - Reference or method used in determining the total nitrogen + * [tot_org_c_meth](tot_org_c_meth.md) - Reference or method used in determining total organic carbon + * [tot_org_carb](tot_org_carb.md) - Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * [tot_part_carb](tot_part_carb.md) - Total particulate carbon content + * [tot_phosp](tot_phosp.md) - Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * [tot_phosphate](tot_phosphate.md) - Total amount or concentration of phosphate + * [tot_sulfur](tot_sulfur.md) - Concentration of total sulfur in the sample + * [train_line](train_line.md) - The subway line name + * [train_stat_loc](train_stat_loc.md) - The train station collection location + * [train_stop_loc](train_stop_loc.md) - The train stop collection location + * [travel_out_six_month](travel_out_six_month.md) - Specification of the countries travelled in the last six months; can include multiple travels + * [turbidity](turbidity.md) - Measure of the amount of cloudiness or haziness in water caused by individual particles + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + * [twin_sibling](twin_sibling.md) - Specification of twin sibling presence + * [typ_occup_density](typ_occup_density.md) - Customary or normal density of occupants + * [urine_collect_meth](urine_collect_meth.md) - Specification of urine collection method + * [urogenit_disord](urogenit_disord.md) - History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * [urogenit_tract_disor](urogenit_tract_disor.md) - History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * [ventilation_rate](ventilation_rate.md) - Ventilation rate of the system in the sampled premises + * [ventilation_type](ventilation_type.md) - Ventilation system used in the sampled premises + * [vfa](vfa.md) - Concentration of Volatile Fatty Acids in the sample + * [vfa_fw](vfa_fw.md) - Original volatile fatty acid concentration in the hydrocarbon resource + * [vis_media](vis_media.md) - The building visual media + * [viscosity](viscosity.md) - A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * [volatile_org_comp](volatile_org_comp.md) - Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * [wall_area](wall_area.md) - The total area of the sampled room's walls + * [wall_const_type](wall_const_type.md) - The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * [wall_finish_mat](wall_finish_mat.md) - The material utilized to finish the outer most layer of the wall + * [wall_height](wall_height.md) - The average height of the walls in the sampled room + * [wall_loc](wall_loc.md) - The relative location of the wall within the room + * [wall_surf_treatment](wall_surf_treatment.md) - The surface treatment of interior wall + * [wall_texture](wall_texture.md) - The feel, appearance, or consistency of a wall surface + * [wall_thermal_mass](wall_thermal_mass.md) - The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * [wall_water_mold](wall_water_mold.md) - Signs of the presence of mold or mildew on a wall + * [wastewater_type](wastewater_type.md) - The origin of wastewater such as human waste, rainfall, storm drains, etc. + * [water_content](water_content.md) - Water content measurement + * [water_content_soil_meth](water_content_soil_meth.md) - Reference or method used in determining the water content of soil + * [water_current](water_current.md) - Measurement of magnitude and direction of flow within a fluid + * [water_cut](water_cut.md) - Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * [water_feat_size](water_feat_size.md) - The size of the water feature + * [water_feat_type](water_feat_type.md) - The type of water feature present within the building being sampled + * [water_production_rate](water_production_rate.md) - Water production rates per well (e.g. 987 m3 / day) + * [water_temp_regm](water_temp_regm.md) - Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [watering_regm](watering_regm.md) - Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [weekday](weekday.md) - The day of the week when sampling occurred + * [weight_loss_3_month](weight_loss_3_month.md) - Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * [win](win.md) - A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * [wind_direction](wind_direction.md) - Wind direction is the direction from which a wind originates + * [wind_speed](wind_speed.md) - Speed of wind measured at the time of sampling + * [window_cond](window_cond.md) - The physical condition of the window at the time of sampling + * [window_cover](window_cover.md) - The type of window covering + * [window_horiz_pos](window_horiz_pos.md) - The horizontal position of the window on the wall + * [window_loc](window_loc.md) - The relative location of the window within the room + * [window_mat](window_mat.md) - The type of material used to finish a window + * [window_open_freq](window_open_freq.md) - The number of times windows are opened per week + * [window_size](window_size.md) - The window's length and width + * [window_status](window_status.md) - Defines whether the windows were open or closed during environmental testing + * [window_type](window_type.md) - The type of windows + * [window_vert_pos](window_vert_pos.md) - The vertical position of the window on the wall + * [window_water_mold](window_water_mold.md) - Signs of the presence of mold or mildew on the window. + * [xylene](xylene.md) - Concentration of xylene in the sample + * [investigation field](investigation_field.md) - field describing aspect of the investigation/study to which the sample belongs + * [experimental_factor](experimental_factor.md) - Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * [ME➞experimental_factor](ME_experimental_factor.md) + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) + * [investigation_type](investigation_type.md) - Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * [ME➞investigation_type](ME_investigation_type.md) + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) + * [MISAG➞investigation_type](MISAG_investigation_type.md) + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) + * [project_name](project_name.md) - Name of the project within which the sequencing was organized + * [ME➞project_name](ME_project_name.md) + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) + * [MIGS org➞project_name](MIGS_org_project_name.md) + * [MIGS plant➞project_name](MIGS_plant_project_name.md) + * [MIGS virus➞project_name](MIGS_virus_project_name.md) + * [MIMAG➞project_name](MIMAG_project_name.md) + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) + * [MISAG➞project_name](MISAG_project_name.md) + * [MIUVIG➞project_name](MIUVIG_project_name.md) + * [sample_name](sample_name.md) - Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * [ME➞sample_name](ME_sample_name.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) + * [MIGS org➞sample_name](MIGS_org_sample_name.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) + * [MIMAG➞sample_name](MIMAG_sample_name.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) + * [MISAG➞sample_name](MISAG_sample_name.md) + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) + * [submitted_to_insdc](submitted_to_insdc.md) - Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) + * [mixs extension field](mixs_extension_field.md) + * [env_package](env_package.md) - MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * [ME➞env_package](ME_env_package.md) + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) + * [MIGS org➞env_package](MIGS_org_env_package.md) + * [MIGS plant➞env_package](MIGS_plant_env_package.md) + * [MIGS virus➞env_package](MIGS_virus_env_package.md) + * [MIMAG➞env_package](MIMAG_env_package.md) + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) + * [MISAG➞env_package](MISAG_env_package.md) + * [MIUVIG➞env_package](MIUVIG_env_package.md) + * [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + * [biotic_relationship](biotic_relationship.md) - Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) + * [encoded_traits](encoded_traits.md) - Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) + * [estimated_size](estimated_size.md) - The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) + * [extrachrom_elements](extrachrom_elements.md) - Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) + * [health_disease_stat](health_disease_stat.md) - Health or disease status of specific host at time of collection + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) + * [host_spec_range](host_spec_range.md) - The NCBI taxonomy identifier of the specific host if it is known + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) + * [isol_growth_condt](isol_growth_condt.md) - Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) + * [num_replicons](num_replicons.md) - Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) + * [pathogenicity](pathogenicity.md) - To what is the entity pathogenic + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) + * [ploidy](ploidy.md) - The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) + * [propagation](propagation.md) - This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) + * [MIGS plant➞propagation](MIGS_plant_propagation.md) + * [MIGS virus➞propagation](MIGS_virus_propagation.md) + * [ref_biomaterial](ref_biomaterial.md) - Primary publication if isolated before genome publication; otherwise, primary genome report + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) + * [rel_to_oxygen](rel_to_oxygen.md) - Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) + * [samp_mat_process](samp_mat_process.md) - A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. + * [ME➞samp_mat_process](ME_samp_mat_process.md) + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) + * [samp_size](samp_size.md) - Amount or size of sample (volume, mass or area) that was collected + * [ME➞samp_size](ME_samp_size.md) + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) + * [MIGS org➞samp_size](MIGS_org_samp_size.md) + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) + * [MIMAG➞samp_size](MIMAG_samp_size.md) + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) + * [MISAG➞samp_size](MISAG_samp_size.md) + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) + * [sample_collect_device](sample_collect_device.md) - The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). + * [ME➞sample_collect_device](ME_sample_collect_device.md) + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) + * [sample_collect_method](sample_collect_method.md) - The method employed for collecting the sample. + * [ME➞sample_collect_method](ME_sample_collect_method.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) + * [size_frac](size_frac.md) - Filtering pore size used in sample preparation + * [ME➞size_frac](ME_size_frac.md) + * [MIMAG➞size_frac](MIMAG_size_frac.md) + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) + * [MISAG➞size_frac](MISAG_size_frac.md) + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) + * [source_mat_id](source_mat_id.md) - A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * [ME➞source_mat_id](ME_source_mat_id.md) + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) + * [source_uvig](source_uvig.md) - Type of dataset from which the UViG was obtained + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) + * [specific_host](specific_host.md) - If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) + * [subspecf_gen_lin](subspecf_gen_lin.md) - This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) + * [trophic_level](trophic_level.md) - Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) + * [virus_enrich_appr](virus_enrich_appr.md) - List of approaches used to enrich the sample for viruses, if any + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) + * [➞has numeric value](quantityValue__has_numeric_value.md) + * [➞has raw value](quantityValue__has_raw_value.md) + * [➞has unit](quantityValue__has_unit.md) - Example "m" + * [sequencing field](sequencing_field.md) + * [adapters](adapters.md) - Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * [ME➞adapters](ME_adapters.md) + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) + * [MIGS org➞adapters](MIGS_org_adapters.md) + * [MIGS plant➞adapters](MIGS_plant_adapters.md) + * [MIGS virus➞adapters](MIGS_virus_adapters.md) + * [MIMAG➞adapters](MIMAG_adapters.md) + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) + * [MISAG➞adapters](MISAG_adapters.md) + * [MIUVIG➞adapters](MIUVIG_adapters.md) + * [annot](annot.md) - Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * [ME➞annot](ME_annot.md) + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) + * [MIGS org➞annot](MIGS_org_annot.md) + * [MIGS plant➞annot](MIGS_plant_annot.md) + * [MIGS virus➞annot](MIGS_virus_annot.md) + * [MIMAG➞annot](MIMAG_annot.md) + * [MISAG➞annot](MISAG_annot.md) + * [MIUVIG➞annot](MIUVIG_annot.md) + * [assembly_name](assembly_name.md) - Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * [ME➞assembly_name](ME_assembly_name.md) + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) + * [MISAG➞assembly_name](MISAG_assembly_name.md) + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) + * [assembly_qual](assembly_qual.md) - The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * [ME➞assembly_qual](ME_assembly_qual.md) + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) + * [assembly_software](assembly_software.md) - Tool(s) used for assembly, including version number and parameters + * [ME➞assembly_software](ME_assembly_software.md) + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) + * [MISAG➞assembly_software](MISAG_assembly_software.md) + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) + * [bin_param](bin_param.md) - The parameters that have been applied during the extraction of genomes from metagenomic datasets + * [MIMAG➞bin_param](MIMAG_bin_param.md) + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) + * [bin_software](bin_software.md) - Tool(s) used for the extraction of genomes from metagenomic datasets + * [MIMAG➞bin_software](MIMAG_bin_software.md) + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) + * [chimera_check](chimera_check.md) - A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) + * [compl_appr](compl_appr.md) - The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) + * [MISAG➞compl_appr](MISAG_compl_appr.md) + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) + * [compl_score](compl_score.md) - Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) + * [MIGS org➞compl_score](MIGS_org_compl_score.md) + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) + * [MIMAG➞compl_score](MIMAG_compl_score.md) + * [MISAG➞compl_score](MISAG_compl_score.md) + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) + * [compl_software](compl_software.md) - Tools used for completion estimate, i.e. checkm, anvi'o, busco + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) + * [MIGS org➞compl_software](MIGS_org_compl_software.md) + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) + * [MIMAG➞compl_software](MIMAG_compl_software.md) + * [MISAG➞compl_software](MISAG_compl_software.md) + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) + * [contam_score](contam_score.md) - The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * [MIMAG➞contam_score](MIMAG_contam_score.md) + * [MISAG➞contam_score](MISAG_contam_score.md) + * [contam_screen_input](contam_screen_input.md) - The type of sequence data used as input + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) + * [contam_screen_param](contam_screen_param.md) - Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) + * [decontam_software](decontam_software.md) - Tool(s) used in contamination screening + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) + * [MISAG➞decontam_software](MISAG_decontam_software.md) + * [detec_type](detec_type.md) - Type of UViG detection + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) + * [feat_pred](feat_pred.md) - Method used to predict UViGs features such as ORFs, integration site, etc. + * [ME➞feat_pred](ME_feat_pred.md) + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) + * [MISAG➞feat_pred](MISAG_feat_pred.md) + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) + * [host_pred_appr](host_pred_appr.md) - Tool or approach used for host prediction + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) + * [host_pred_est_acc](host_pred_est_acc.md) - For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) + * [lib_layout](lib_layout.md) - Specify whether to expect single, paired, or other configuration of reads + * [ME➞lib_layout](ME_lib_layout.md) + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) + * [MISAG➞lib_layout](MISAG_lib_layout.md) + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) + * [lib_reads_seqd](lib_reads_seqd.md) - Total number of clones sequenced from the library + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) + * [lib_screen](lib_screen.md) - Specific enrichment or screening methods applied before and/or after creating libraries + * [ME➞lib_screen](ME_lib_screen.md) + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) + * [MISAG➞lib_screen](MISAG_lib_screen.md) + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) + * [lib_size](lib_size.md) - Total number of clones in the library prepared for the project + * [ME➞lib_size](ME_lib_size.md) + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) + * [MIGS org➞lib_size](MIGS_org_lib_size.md) + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) + * [MIMAG➞lib_size](MIMAG_lib_size.md) + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) + * [MISAG➞lib_size](MISAG_lib_size.md) + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) + * [lib_vector](lib_vector.md) - Cloning vector type(s) used in construction of libraries + * [ME➞lib_vector](ME_lib_vector.md) + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) + * [MISAG➞lib_vector](MISAG_lib_vector.md) + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) + * [mag_cov_software](mag_cov_software.md) - Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) + * [mid](mid.md) - Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * [ME➞mid](ME_mid.md) + * [MIMAG➞mid](MIMAG_mid.md) + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) + * [MISAG➞mid](MISAG_mid.md) + * [MIUVIG➞mid](MIUVIG_mid.md) + * [nucl_acid_amp](nucl_acid_amp.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) + * [nucl_acid_ext](nucl_acid_ext.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) + * [number_contig](number_contig.md) - Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * [ME➞number_contig](ME_number_contig.md) + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) + * [MIGS org➞number_contig](MIGS_org_number_contig.md) + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) + * [MIMAG➞number_contig](MIMAG_number_contig.md) + * [MISAG➞number_contig](MISAG_number_contig.md) + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) + * [pcr_cond](pcr_cond.md) - Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) + * [pcr_primers](pcr_primers.md) - PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) + * [pred_genome_struc](pred_genome_struc.md) - Expected structure of the viral genome + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) + * [pred_genome_type](pred_genome_type.md) - Type of genome predicted for the UViG + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) + * [reassembly_bin](reassembly_bin.md) - Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) + * [ref_db](ref_db.md) - List of database(s) used for ORF annotation, along with version number and reference to website or publication + * [ME➞ref_db](ME_ref_db.md) + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) + * [MIGS org➞ref_db](MIGS_org_ref_db.md) + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) + * [MIMAG➞ref_db](MIMAG_ref_db.md) + * [MISAG➞ref_db](MISAG_ref_db.md) + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) + * [seq_meth](seq_meth.md) - Sequencing method used; e.g. Sanger, ABI-solid + * [ME➞seq_meth](ME_seq_meth.md) + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) + * [MISAG➞seq_meth](MISAG_seq_meth.md) + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) + * [seq_quality_check](seq_quality_check.md) - Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) + * [sim_search_meth](sim_search_meth.md) - Tool used to compare ORFs with database, along with version and cutoffs used + * [ME➞sim_search_meth](ME_sim_search_meth.md) + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) + * [single_cell_lysis_appr](single_cell_lysis_appr.md) - Method used to free DNA from interior of the cell(s) or particle(s) + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) + * [single_cell_lysis_prot](single_cell_lysis_prot.md) - Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) + * [sop](sop.md) - Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * [ME➞sop](ME_sop.md) + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) + * [MIGS org➞sop](MIGS_org_sop.md) + * [MIGS plant➞sop](MIGS_plant_sop.md) + * [MIGS virus➞sop](MIGS_virus_sop.md) + * [MIMAG➞sop](MIMAG_sop.md) + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) + * [MISAG➞sop](MISAG_sop.md) + * [MIUVIG➞sop](MIUVIG_sop.md) + * [sort_tech](sort_tech.md) - Method used to sort/isolate cells or particles of interest + * [MISAG➞sort_tech](MISAG_sort_tech.md) + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) + * [target_gene](target_gene.md) - Targeted gene or locus name for marker gene studies + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) + * [target_subfragment](target_subfragment.md) - Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) + * [tax_class](tax_class.md) - Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * [ME➞tax_class](ME_tax_class.md) + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) + * [MIGS org➞tax_class](MIGS_org_tax_class.md) + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) + * [MIMAG➞tax_class](MIMAG_tax_class.md) + * [MISAG➞tax_class](MISAG_tax_class.md) + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) + * [tax_ident](tax_ident.md) - The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) + * [MISAG➞tax_ident](MISAG_tax_ident.md) + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) + * [trna_ext_software](trna_ext_software.md) - Tools used for tRNA identification + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) + * [trnas](trnas.md) - The total number of tRNAs identified from the SAG or MAG + * [MIMAG➞trnas](MIMAG_trnas.md) + * [MISAG➞trnas](MISAG_trnas.md) + * [MIUVIG➞trnas](MIUVIG_trnas.md) + * [url](url.md) + * [ME➞url](ME_url.md) + * [MIGS bacteria➞url](MIGS_bacteria_url.md) + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) + * [MIGS org➞url](MIGS_org_url.md) + * [MIGS plant➞url](MIGS_plant_url.md) + * [MIGS virus➞url](MIGS_virus_url.md) + * [MIMAG➞url](MIMAG_url.md) + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) + * [MIMARKS survey➞url](MIMARKS_survey_url.md) + * [MISAG➞url](MISAG_url.md) + * [MIUVIG➞url](MIUVIG_url.md) + * [vir_ident_software](vir_ident_software.md) - Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) + * [votu_class_appr](votu_class_appr.md) - Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) + * [votu_db](votu_db.md) - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) + * [votu_seq_comp_appr](votu_seq_comp_appr.md) - Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) + * [wga_amp_appr](wga_amp_appr.md) - Method used to amplify genomic DNA in preparation for sequencing + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) + * [wga_amp_kit](wga_amp_kit.md) - Kit used to amplify genomic DNA in preparation for sequencing + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) + * [x_16s_recover](x_16s_recover.md) - Can a 16S gene be recovered from the submitted SAG or MAG? + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) + +### Enums + + * [add_recov_method_enum](add_recov_method_enum.md) + * [arch_struc_enum](arch_struc_enum.md) + * [assembly_qual_enum](assembly_qual_enum.md) + * [bin_param_enum](bin_param_enum.md) + * [bin_software_enum](bin_software_enum.md) + * [biol_stat_enum](biol_stat_enum.md) + * [biotic_relationship_enum](biotic_relationship_enum.md) + * [build_docs_enum](build_docs_enum.md) + * [build_occup_type_enum](build_occup_type_enum.md) + * [building_setting_enum](building_setting_enum.md) + * [ceil_cond_enum](ceil_cond_enum.md) + * [ceil_finish_mat_enum](ceil_finish_mat_enum.md) + * [ceil_texture_enum](ceil_texture_enum.md) + * [ceil_type_enum](ceil_type_enum.md) + * [compl_appr_enum](compl_appr_enum.md) + * [compl_score_enum](compl_score_enum.md) + * [contam_screen_param_enum](contam_screen_param_enum.md) + * [cur_land_use_enum](cur_land_use_enum.md) + * [decontam_software_enum](decontam_software_enum.md) + * [depos_env_enum](depos_env_enum.md) + * [dominant_hand_enum](dominant_hand_enum.md) + * [door_comp_type_enum](door_comp_type_enum.md) + * [door_cond_enum](door_cond_enum.md) + * [door_direct_enum](door_direct_enum.md) + * [door_loc_enum](door_loc_enum.md) + * [door_mat_enum](door_mat_enum.md) + * [door_move_enum](door_move_enum.md) + * [door_type_enum](door_type_enum.md) + * [door_type_metal_enum](door_type_metal_enum.md) + * [door_type_wood_enum](door_type_wood_enum.md) + * [drainage_class_enum](drainage_class_enum.md) + * [drawings_enum](drawings_enum.md) + * [drug_usage_enum](drug_usage_enum.md) + * [env_package_enum](env_package_enum.md) + * [ext_wall_orient_enum](ext_wall_orient_enum.md) + * [ext_window_orient_enum](ext_window_orient_enum.md) + * [fao_class_enum](fao_class_enum.md) + * [filter_type_enum](filter_type_enum.md) + * [floor_cond_enum](floor_cond_enum.md) + * [floor_finish_mat_enum](floor_finish_mat_enum.md) + * [floor_struc_enum](floor_struc_enum.md) + * [floor_water_mold_enum](floor_water_mold_enum.md) + * [furniture_enum](furniture_enum.md) + * [growth_habit_enum](growth_habit_enum.md) + * [handidness_enum](handidness_enum.md) + * [hc_produced_enum](hc_produced_enum.md) + * [hcr_enum](hcr_enum.md) + * [hcr_geol_age_enum](hcr_geol_age_enum.md) + * [health_disease_stat_enum](health_disease_stat_enum.md) + * [heat_cool_type_enum](heat_cool_type_enum.md) + * [heat_deliv_loc_enum](heat_deliv_loc_enum.md) + * [horizon_enum](horizon_enum.md) + * [host_pred_appr_enum](host_pred_appr_enum.md) + * [host_sex_enum](host_sex_enum.md) + * [indoor_space_enum](indoor_space_enum.md) + * [indoor_surf_enum](indoor_surf_enum.md) + * [int_wall_cond_enum](int_wall_cond_enum.md) + * [investigation_type_enum](investigation_type_enum.md) + * [lib_layout_enum](lib_layout_enum.md) + * [light_type_enum](light_type_enum.md) + * [lithology_enum](lithology_enum.md) + * [mag_cov_software_enum](mag_cov_software_enum.md) + * [mech_struc_enum](mech_struc_enum.md) + * [occup_document_enum](occup_document_enum.md) + * [organism_count_enum](organism_count_enum.md) + * [oxy_stat_samp_enum](oxy_stat_samp_enum.md) + * [plant_growth_med_enum](plant_growth_med_enum.md) + * [plant_sex_enum](plant_sex_enum.md) + * [pred_genome_struc_enum](pred_genome_struc_enum.md) + * [pred_genome_type_enum](pred_genome_type_enum.md) + * [pres_animal_enum](pres_animal_enum.md) + * [profile_position_enum](profile_position_enum.md) + * [quad_pos_enum](quad_pos_enum.md) + * [rel_samp_loc_enum](rel_samp_loc_enum.md) + * [rel_to_oxygen_enum](rel_to_oxygen_enum.md) + * [room_condt_enum](room_condt_enum.md) + * [room_connected_enum](room_connected_enum.md) + * [room_loc_enum](room_loc_enum.md) + * [room_samp_pos_enum](room_samp_pos_enum.md) + * [room_type_enum](room_type_enum.md) + * [samp_capt_status_enum](samp_capt_status_enum.md) + * [samp_collection_point_enum](samp_collection_point_enum.md) + * [samp_dis_stage_enum](samp_dis_stage_enum.md) + * [samp_floor_enum](samp_floor_enum.md) + * [samp_md_enum](samp_md_enum.md) + * [samp_subtype_enum](samp_subtype_enum.md) + * [samp_type_enum](samp_type_enum.md) + * [samp_weather_enum](samp_weather_enum.md) + * [season_use_enum](season_use_enum.md) + * [sediment_type_enum](sediment_type_enum.md) + * [seq_meth_enum](seq_meth_enum.md) + * [shading_device_cond_enum](shading_device_cond_enum.md) + * [shading_device_type_enum](shading_device_type_enum.md) + * [single_cell_lysis_appr_enum](single_cell_lysis_appr_enum.md) + * [sort_tech_enum](sort_tech_enum.md) + * [source_uvig_enum](source_uvig_enum.md) + * [special_diet_enum](special_diet_enum.md) + * [specific_enum](specific_enum.md) + * [sr_dep_env_enum](sr_dep_env_enum.md) + * [sr_geol_age_enum](sr_geol_age_enum.md) + * [sr_kerog_type_enum](sr_kerog_type_enum.md) + * [sr_lithology_enum](sr_lithology_enum.md) + * [study_complt_stat_enum](study_complt_stat_enum.md) + * [substructure_type_enum](substructure_type_enum.md) + * [surf_air_cont_enum](surf_air_cont_enum.md) + * [surf_material_enum](surf_material_enum.md) + * [tax_ident_enum](tax_ident_enum.md) + * [tidal_stage_enum](tidal_stage_enum.md) + * [tillage_enum](tillage_enum.md) + * [train_line_enum](train_line_enum.md) + * [train_stat_loc_enum](train_stat_loc_enum.md) + * [train_stop_loc_enum](train_stop_loc_enum.md) + * [trophic_level_enum](trophic_level_enum.md) + * [virus_enrich_appr_enum](virus_enrich_appr_enum.md) + * [vis_media_enum](vis_media_enum.md) + * [wall_const_type_enum](wall_const_type_enum.md) + * [wall_finish_mat_enum](wall_finish_mat_enum.md) + * [wall_loc_enum](wall_loc_enum.md) + * [wall_surf_treatment_enum](wall_surf_treatment_enum.md) + * [wall_texture_enum](wall_texture_enum.md) + * [water_feat_type_enum](water_feat_type_enum.md) + * [weekday_enum](weekday_enum.md) + * [window_cond_enum](window_cond_enum.md) + * [window_cover_enum](window_cover_enum.md) + * [window_horiz_pos_enum](window_horiz_pos_enum.md) + * [window_loc_enum](window_loc_enum.md) + * [window_mat_enum](window_mat_enum.md) + * [window_type_enum](window_type_enum.md) + * [window_vert_pos_enum](window_vert_pos_enum.md) + +### Types + + +#### Built in + + * **Bool** + * **Decimal** + * **ElementIdentifier** + * **NCName** + * **NodeIdentifier** + * **URI** + * **URIorCURIE** + * **XSDDate** + * **XSDDateTime** + * **XSDTime** + * **float** + * **int** + * **str** + +#### Defined + + * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value + * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar + * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time + * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification + * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification + * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification + * [Integer](types/Integer.md) (**int**) - An integer + * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE + * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. + * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. + * [String](types/String.md) (**str**) - A character string + * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day + * [Uri](types/Uri.md) (**URI**) - a complete URI + * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/mixs6/indoor_space.md b/mixs6/indoor_space.md new file mode 100644 index 00000000..a6314ef6 --- /dev/null +++ b/mixs6/indoor_space.md @@ -0,0 +1,47 @@ + +# Slot: indoor_space + + +A distinguishable space within a structure, the purpose for which discrete areas of a building is used + +URI: [mixs.vocab:indoor_space](https://w3id.org/mixs/vocab/indoor_space) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | indoor space | +| **Mappings:** | | MIXS:0000763 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 15.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='foyer', description=None) | + diff --git a/mixs6/indoor_surf.md b/mixs6/indoor_surf.md new file mode 100644 index 00000000..740be8b6 --- /dev/null +++ b/mixs6/indoor_surf.md @@ -0,0 +1,47 @@ + +# Slot: indoor_surf + + +Type of indoor surface + +URI: [mixs.vocab:indoor_surf](https://w3id.org/mixs/vocab/indoor_surf) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | indoor surface | +| **Mappings:** | | MIXS:0000764 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 16.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wall', description=None) | + diff --git a/mixs6/indust_eff_percent.md b/mixs6/indust_eff_percent.md new file mode 100644 index 00000000..0ed84035 --- /dev/null +++ b/mixs6/indust_eff_percent.md @@ -0,0 +1,48 @@ + +# Slot: indust_eff_percent + + +Percentage of industrial effluents received by wastewater treatment plant + +URI: [mixs.vocab:indust_eff_percent](https://w3id.org/mixs/vocab/indust_eff_percent) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | industrial effluent percent | +| **Mappings:** | | MIXS:0000662 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/inorg_particles.md b/mixs6/inorg_particles.md new file mode 100644 index 00000000..a2155917 --- /dev/null +++ b/mixs6/inorg_particles.md @@ -0,0 +1,48 @@ + +# Slot: inorg_particles + + +Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + +URI: [mixs.vocab:inorg_particles](https://w3id.org/mixs/vocab/inorg_particles) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | inorganic particles | +| **Mappings:** | | MIXS:0000664 | +| **Comments:** | | Expected value: inorganic particle name;measurement value | +| | | Preferred unit: mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/inside_lux.md b/mixs6/inside_lux.md new file mode 100644 index 00000000..92515128 --- /dev/null +++ b/mixs6/inside_lux.md @@ -0,0 +1,48 @@ + +# Slot: inside_lux + + +The recorded value at sampling time (power density) + +URI: [mixs.vocab:inside_lux](https://w3id.org/mixs/vocab/inside_lux) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | inside lux light | +| **Mappings:** | | MIXS:0000168 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilowatt per square metre | +| | | Occurrence: 1 | +| | | Position: 87.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/int_wall_cond.md b/mixs6/int_wall_cond.md new file mode 100644 index 00000000..8772d356 --- /dev/null +++ b/mixs6/int_wall_cond.md @@ -0,0 +1,47 @@ + +# Slot: int_wall_cond + + +The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + +URI: [mixs.vocab:int_wall_cond](https://w3id.org/mixs/vocab/int_wall_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | interior wall condition | +| **Mappings:** | | MIXS:0000813 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 88.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='damaged', description=None) | + diff --git a/mixs6/investigation_field.md b/mixs6/investigation_field.md new file mode 100644 index 00000000..96f6808f --- /dev/null +++ b/mixs6/investigation_field.md @@ -0,0 +1,26 @@ + +# Slot: investigation_field + + +field describing aspect of the investigation/study to which the sample belongs + +URI: [mixs.vocab:investigation_field](https://w3id.org/mixs/vocab/investigation_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [experimental_factor](experimental_factor.md) + * [investigation_type](investigation_type.md) + * [project_name](project_name.md) + * [sample_name](sample_name.md) + * [submitted_to_insdc](submitted_to_insdc.md) + +## Used by + diff --git a/mixs6/investigation_type.md b/mixs6/investigation_type.md new file mode 100644 index 00000000..10d4647b --- /dev/null +++ b/mixs6/investigation_type.md @@ -0,0 +1,45 @@ + +# Slot: investigation_type + + +Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + +URI: [mixs.vocab:investigation_type](https://w3id.org/mixs/vocab/investigation_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + * [ME➞investigation_type](ME_investigation_type.md) + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) + * [MISAG➞investigation_type](MISAG_investigation_type.md) + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | investigation type | +| **Comments:** | | Expected value: eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genomes | +| | | Position: 2.0 | +| **Examples:** | | Example(value='metagenome', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/60 | + diff --git a/mixs6/isol_growth_condt.md b/mixs6/isol_growth_condt.md new file mode 100644 index 00000000..67b453a9 --- /dev/null +++ b/mixs6/isol_growth_condt.md @@ -0,0 +1,39 @@ + +# Slot: isol_growth_condt + + +Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + +URI: [mixs.vocab:isol_growth_condt](https://w3id.org/mixs/vocab/isol_growth_condt) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | isolation and growth condition | +| **Comments:** | | Expected value: PMID,DOI or URL | +| | | Position: 30.0 | +| **Examples:** | | Example(value='doi: 10.1016/j.syapm.2018.01.009', description=None) | + diff --git a/mixs6/iw_bt_date_well.md b/mixs6/iw_bt_date_well.md new file mode 100644 index 00000000..07824676 --- /dev/null +++ b/mixs6/iw_bt_date_well.md @@ -0,0 +1,47 @@ + +# Slot: iw_bt_date_well + + +Injection water breakthrough date per well following a secondary and/or tertiary recovery + +URI: [mixs.vocab:iw_bt_date_well](https://w3id.org/mixs/vocab/iw_bt_date_well) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | injection water breakthrough date of specific well | +| **Mappings:** | | MIXS:0001010 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 29.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/iwf.md b/mixs6/iwf.md new file mode 100644 index 00000000..1c441ad6 --- /dev/null +++ b/mixs6/iwf.md @@ -0,0 +1,48 @@ + +# Slot: iwf + + +Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + +URI: [mixs.vocab:iwf](https://w3id.org/mixs/vocab/iwf) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | injection water fraction | +| **Mappings:** | | MIXS:0000455 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 27.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/kidney_disord.md b/mixs6/kidney_disord.md new file mode 100644 index 00000000..ef63a25f --- /dev/null +++ b/mixs6/kidney_disord.md @@ -0,0 +1,47 @@ + +# Slot: kidney_disord + + +History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + +URI: [mixs.vocab:kidney_disord](https://w3id.org/mixs/vocab/kidney_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urine/kidney disorder | +| **Mappings:** | | MIXS:0000277 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 40.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/last_clean.md b/mixs6/last_clean.md new file mode 100644 index 00000000..3ac71306 --- /dev/null +++ b/mixs6/last_clean.md @@ -0,0 +1,47 @@ + +# Slot: last_clean + + +The last time the floor was cleaned (swept, mopped, vacuumed) + +URI: [mixs.vocab:last_clean](https://w3id.org/mixs/vocab/last_clean) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | last time swept/mopped/vacuumed | +| **Mappings:** | | MIXS:0000814 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 89.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2018-05-11:T14:30Z', description=None) | + diff --git a/mixs6/lat_lon.md b/mixs6/lat_lon.md new file mode 100644 index 00000000..160fcf6e --- /dev/null +++ b/mixs6/lat_lon.md @@ -0,0 +1,249 @@ + +# Slot: lat_lon + + +The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + +URI: [mixs.vocab:lat_lon](https://w3id.org/mixs/vocab/lat_lon) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + * [ME➞lat_lon](ME_lat_lon.md) + * [MIGS bacteria➞lat_lon](MIGS_bacteria_lat_lon.md) + * [MIGS eukaryote➞lat_lon](MIGS_eukaryote_lat_lon.md) + * [MIGS org➞lat_lon](MIGS_org_lat_lon.md) + * [MIGS plant➞lat_lon](MIGS_plant_lat_lon.md) + * [MIGS virus➞lat_lon](MIGS_virus_lat_lon.md) + * [MIMAG➞lat_lon](MIMAG_lat_lon.md) + * [MIMARKS specimen➞lat_lon](MIMARKS_specimen_lat_lon.md) + * [MIMARKS survey➞lat_lon](MIMARKS_survey_lat_lon.md) + * [MISAG➞lat_lon](MISAG_lat_lon.md) + * [MIUVIG➞lat_lon](MIUVIG_lat_lon.md) + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Core](Core.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | geographic location (latitude and longitude) | +| **Comments:** | | Expected value: decimal degrees | +| | | Position: 5.0 | +| **Examples:** | | Example(value='50.586825 6.408977', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/62 | + diff --git a/mixs6/lib_layout.md b/mixs6/lib_layout.md new file mode 100644 index 00000000..eb667bbb --- /dev/null +++ b/mixs6/lib_layout.md @@ -0,0 +1,43 @@ + +# Slot: lib_layout + + +Specify whether to expect single, paired, or other configuration of reads + +URI: [mixs.vocab:lib_layout](https://w3id.org/mixs/vocab/lib_layout) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞lib_layout](ME_lib_layout.md) + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) + * [MISAG➞lib_layout](MISAG_lib_layout.md) + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library layout | +| **Comments:** | | Expected value: enumeration | +| | | Position: 41.0 | +| **Examples:** | | Example(value='paired', description=None) | + diff --git a/mixs6/lib_reads_seqd.md b/mixs6/lib_reads_seqd.md new file mode 100644 index 00000000..656f1d10 --- /dev/null +++ b/mixs6/lib_reads_seqd.md @@ -0,0 +1,43 @@ + +# Slot: lib_reads_seqd + + +Total number of clones sequenced from the library + +URI: [mixs.vocab:lib_reads_seqd](https://w3id.org/mixs/vocab/lib_reads_seqd) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library reads sequenced | +| **Comments:** | | Expected value: number of reads sequenced | +| | | Position: 40.0 | +| **Examples:** | | Example(value='20', description=None) | + diff --git a/mixs6/lib_screen.md b/mixs6/lib_screen.md new file mode 100644 index 00000000..577fd0aa --- /dev/null +++ b/mixs6/lib_screen.md @@ -0,0 +1,43 @@ + +# Slot: lib_screen + + +Specific enrichment or screening methods applied before and/or after creating libraries + +URI: [mixs.vocab:lib_screen](https://w3id.org/mixs/vocab/lib_screen) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞lib_screen](ME_lib_screen.md) + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) + * [MISAG➞lib_screen](MISAG_lib_screen.md) + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library screening strategy | +| **Comments:** | | Expected value: screening strategy name | +| | | Position: 43.0 | +| **Examples:** | | Example(value='enriched, screened, normalized', description=None) | + diff --git a/mixs6/lib_size.md b/mixs6/lib_size.md new file mode 100644 index 00000000..8b9400a2 --- /dev/null +++ b/mixs6/lib_size.md @@ -0,0 +1,43 @@ + +# Slot: lib_size + + +Total number of clones in the library prepared for the project + +URI: [mixs.vocab:lib_size](https://w3id.org/mixs/vocab/lib_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞lib_size](ME_lib_size.md) + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) + * [MIGS org➞lib_size](MIGS_org_lib_size.md) + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) + * [MIMAG➞lib_size](MIMAG_lib_size.md) + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) + * [MISAG➞lib_size](MISAG_lib_size.md) + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library size | +| **Comments:** | | Expected value: number of clones | +| | | Position: 39.0 | +| **Examples:** | | Example(value='50', description=None) | + diff --git a/mixs6/lib_vector.md b/mixs6/lib_vector.md new file mode 100644 index 00000000..ed175c6a --- /dev/null +++ b/mixs6/lib_vector.md @@ -0,0 +1,43 @@ + +# Slot: lib_vector + + +Cloning vector type(s) used in construction of libraries + +URI: [mixs.vocab:lib_vector](https://w3id.org/mixs/vocab/lib_vector) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞lib_vector](ME_lib_vector.md) + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) + * [MISAG➞lib_vector](MISAG_lib_vector.md) + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library vector | +| **Comments:** | | Expected value: vector | +| | | Position: 42.0 | +| **Examples:** | | Example(value='Bacteriophage P1', description=None) | + diff --git a/mixs6/light_intensity.md b/mixs6/light_intensity.md new file mode 100644 index 00000000..4e527bc5 --- /dev/null +++ b/mixs6/light_intensity.md @@ -0,0 +1,48 @@ + +# Slot: light_intensity + + +Measurement of light intensity + +URI: [mixs.vocab:light_intensity](https://w3id.org/mixs/vocab/light_intensity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | light intensity | +| **Mappings:** | | MIXS:0000706 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: lux | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.3 lux', description=None) | + diff --git a/mixs6/light_regm.md b/mixs6/light_regm.md new file mode 100644 index 00000000..c33d4e51 --- /dev/null +++ b/mixs6/light_regm.md @@ -0,0 +1,48 @@ + +# Slot: light_regm + + +Information about treatment(s) involving exposure to light, including both light intensity and quality. + +URI: [mixs.vocab:light_regm](https://w3id.org/mixs/vocab/light_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | light regimen | +| **Mappings:** | | MIXS:0000569 | +| **Comments:** | | Expected value: exposure type;light intensity;light quality | +| | | Preferred unit: lux; micrometer, nanometer, angstrom | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='incandescant light;10 lux;450 nanometer', description=None) | + diff --git a/mixs6/light_type.md b/mixs6/light_type.md new file mode 100644 index 00000000..3e617938 --- /dev/null +++ b/mixs6/light_type.md @@ -0,0 +1,47 @@ + +# Slot: light_type + + +Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + +URI: [mixs.vocab:light_type](https://w3id.org/mixs/vocab/light_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | light type | +| **Mappings:** | | MIXS:0000769 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 21.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='desk lamp', description=None) | + diff --git a/mixs6/link_addit_analys.md b/mixs6/link_addit_analys.md new file mode 100644 index 00000000..04d9c501 --- /dev/null +++ b/mixs6/link_addit_analys.md @@ -0,0 +1,47 @@ + +# Slot: link_addit_analys + + +Link to additional analysis results performed on the sample + +URI: [mixs.vocab:link_addit_analys](https://w3id.org/mixs/vocab/link_addit_analys) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | links to additional analysis | +| **Mappings:** | | MIXS:0000340 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 45.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/link_class_info.md b/mixs6/link_class_info.md new file mode 100644 index 00000000..dd7dfb21 --- /dev/null +++ b/mixs6/link_class_info.md @@ -0,0 +1,47 @@ + +# Slot: link_class_info + + +Link to digitized soil maps or other soil classification information + +URI: [mixs.vocab:link_class_info](https://w3id.org/mixs/vocab/link_class_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | link to classification information | +| **Mappings:** | | MIXS:0000329 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 25.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/link_climate_info.md b/mixs6/link_climate_info.md new file mode 100644 index 00000000..9cf5d4d9 --- /dev/null +++ b/mixs6/link_climate_info.md @@ -0,0 +1,47 @@ + +# Slot: link_climate_info + + +Link to climate resource + +URI: [mixs.vocab:link_climate_info](https://w3id.org/mixs/vocab/link_climate_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | link to climate information | +| **Mappings:** | | MIXS:0000328 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 20.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/lithology.md b/mixs6/lithology.md new file mode 100644 index 00000000..95a86c18 --- /dev/null +++ b/mixs6/lithology.md @@ -0,0 +1,59 @@ + +# Slot: lithology + + +Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:lithology](https://w3id.org/mixs/vocab/lithology) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | lithology | +| **Mappings:** | | MIXS:0000990 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 12.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Volcanic', description=None) | + diff --git a/mixs6/liver_disord.md b/mixs6/liver_disord.md new file mode 100644 index 00000000..1edbc172 --- /dev/null +++ b/mixs6/liver_disord.md @@ -0,0 +1,47 @@ + +# Slot: liver_disord + + +History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + +URI: [mixs.vocab:liver_disord](https://w3id.org/mixs/vocab/liver_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | liver disorder | +| **Mappings:** | | MIXS:0000282 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 2.0 | +| | | This field is used uniquely in: human-gut | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/local_class.md b/mixs6/local_class.md new file mode 100644 index 00000000..d9470282 --- /dev/null +++ b/mixs6/local_class.md @@ -0,0 +1,47 @@ + +# Slot: local_class + + +Soil classification based on local soil classification system + +URI: [mixs.vocab:local_class](https://w3id.org/mixs/vocab/local_class) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil_taxonomic/local classification | +| **Mappings:** | | MIXS:0000330 | +| **Comments:** | | Expected value: local classification name | +| | | Occurrence: 1 | +| | | Position: 27.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/local_class_meth.md b/mixs6/local_class_meth.md new file mode 100644 index 00000000..cc3da0c6 --- /dev/null +++ b/mixs6/local_class_meth.md @@ -0,0 +1,47 @@ + +# Slot: local_class_meth + + +Reference or method used in determining the local soil classification + +URI: [mixs.vocab:local_class_meth](https://w3id.org/mixs/vocab/local_class_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil_taxonomic/local classification method | +| **Mappings:** | | MIXS:0000331 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 28.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/mag_cov_software.md b/mixs6/mag_cov_software.md new file mode 100644 index 00000000..355ac8f7 --- /dev/null +++ b/mixs6/mag_cov_software.md @@ -0,0 +1,35 @@ + +# Slot: mag_cov_software + + +Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + +URI: [mixs.vocab:mag_cov_software](https://w3id.org/mixs/vocab/mag_cov_software) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MAG coverage software | +| **Comments:** | | Expected value: enumeration | +| | | Position: 82.0 | +| **Examples:** | | Example(value='bbmap', description=None) | + diff --git a/mixs6/magnesium.md b/mixs6/magnesium.md new file mode 100644 index 00000000..810cca11 --- /dev/null +++ b/mixs6/magnesium.md @@ -0,0 +1,96 @@ + +# Slot: magnesium + + +Concentration of magnesium in the sample + +URI: [mixs.vocab:magnesium](https://w3id.org/mixs/vocab/magnesium) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | magnesium | +| **Mappings:** | | MIXS:0000431 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mole per liter, milligram per liter, parts per million, micromole per kilogram | +| | | Occurrence: 1 | +| | | Position: 69.0 | +| | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='52.8 micromole per kilogram', description=None) | + diff --git a/mixs6/maternal_health_stat.md b/mixs6/maternal_health_stat.md new file mode 100644 index 00000000..1fac52f5 --- /dev/null +++ b/mixs6/maternal_health_stat.md @@ -0,0 +1,47 @@ + +# Slot: maternal_health_stat + + +Specification of the maternal health status + +URI: [mixs.vocab:maternal_health_stat](https://w3id.org/mixs/vocab/maternal_health_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/maternal health status | +| **Mappings:** | | MIXS:0000273 | +| **Comments:** | | Expected value: health status | +| | | Occurrence: 1 | +| | | Position: 37.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/max_occup.md b/mixs6/max_occup.md new file mode 100644 index 00000000..c3c33e8e --- /dev/null +++ b/mixs6/max_occup.md @@ -0,0 +1,47 @@ + +# Slot: max_occup + + +The maximum amount of people allowed in the indoor environment + +URI: [mixs.vocab:max_occup](https://w3id.org/mixs/vocab/max_occup) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | maximum occupancy | +| **Mappings:** | | MIXS:0000229 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 90.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/me_adapters.md b/mixs6/me_adapters.md new file mode 100644 index 00000000..526edf17 --- /dev/null +++ b/mixs6/me_adapters.md @@ -0,0 +1,47 @@ + +# Slot: ME_adapters + + + + +URI: [mixs.vocab:ME_adapters](https://w3id.org/mixs/vocab/ME_adapters) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_annot.md b/mixs6/me_annot.md new file mode 100644 index 00000000..13c11660 --- /dev/null +++ b/mixs6/me_annot.md @@ -0,0 +1,47 @@ + +# Slot: ME_annot + + + + +URI: [mixs.vocab:ME_annot](https://w3id.org/mixs/vocab/ME_annot) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_assembly_name.md b/mixs6/me_assembly_name.md new file mode 100644 index 00000000..f896238f --- /dev/null +++ b/mixs6/me_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: ME_assembly_name + + + + +URI: [mixs.vocab:ME_assembly_name](https://w3id.org/mixs/vocab/ME_assembly_name) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_assembly_qual.md b/mixs6/me_assembly_qual.md new file mode 100644 index 00000000..93adbb66 --- /dev/null +++ b/mixs6/me_assembly_qual.md @@ -0,0 +1,47 @@ + +# Slot: ME_assembly_qual + + + + +URI: [mixs.vocab:ME_assembly_qual](https://w3id.org/mixs/vocab/ME_assembly_qual) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_assembly_software.md b/mixs6/me_assembly_software.md new file mode 100644 index 00000000..42ea280f --- /dev/null +++ b/mixs6/me_assembly_software.md @@ -0,0 +1,47 @@ + +# Slot: ME_assembly_software + + + + +URI: [mixs.vocab:ME_assembly_software](https://w3id.org/mixs/vocab/ME_assembly_software) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_collection_date.md b/mixs6/me_collection_date.md new file mode 100644 index 00000000..36cf2144 --- /dev/null +++ b/mixs6/me_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: ME_collection_date + + + + +URI: [mixs.vocab:ME_collection_date](https://w3id.org/mixs/vocab/ME_collection_date) + + +## Domain and Range + +[ME](ME.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_broad_scale.md b/mixs6/me_env_broad_scale.md new file mode 100644 index 00000000..1b9efbe2 --- /dev/null +++ b/mixs6/me_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: ME_env_broad_scale + + + + +URI: [mixs.vocab:ME_env_broad_scale](https://w3id.org/mixs/vocab/ME_env_broad_scale) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_local_scale.md b/mixs6/me_env_local_scale.md new file mode 100644 index 00000000..1373bef6 --- /dev/null +++ b/mixs6/me_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: ME_env_local_scale + + + + +URI: [mixs.vocab:ME_env_local_scale](https://w3id.org/mixs/vocab/ME_env_local_scale) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_medium.md b/mixs6/me_env_medium.md new file mode 100644 index 00000000..0ec09fe4 --- /dev/null +++ b/mixs6/me_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: ME_env_medium + + + + +URI: [mixs.vocab:ME_env_medium](https://w3id.org/mixs/vocab/ME_env_medium) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_package.md b/mixs6/me_env_package.md new file mode 100644 index 00000000..7275e02f --- /dev/null +++ b/mixs6/me_env_package.md @@ -0,0 +1,47 @@ + +# Slot: ME_env_package + + + + +URI: [mixs.vocab:ME_env_package](https://w3id.org/mixs/vocab/ME_env_package) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_experimental_factor.md b/mixs6/me_experimental_factor.md new file mode 100644 index 00000000..cf74336d --- /dev/null +++ b/mixs6/me_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: ME_experimental_factor + + + + +URI: [mixs.vocab:ME_experimental_factor](https://w3id.org/mixs/vocab/ME_experimental_factor) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_feat_pred.md b/mixs6/me_feat_pred.md new file mode 100644 index 00000000..cc611ca0 --- /dev/null +++ b/mixs6/me_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: ME_feat_pred + + + + +URI: [mixs.vocab:ME_feat_pred](https://w3id.org/mixs/vocab/ME_feat_pred) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_geo_loc_name.md b/mixs6/me_geo_loc_name.md new file mode 100644 index 00000000..e2981e26 --- /dev/null +++ b/mixs6/me_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: ME_geo_loc_name + + + + +URI: [mixs.vocab:ME_geo_loc_name](https://w3id.org/mixs/vocab/ME_geo_loc_name) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_investigation_type.md b/mixs6/me_investigation_type.md new file mode 100644 index 00000000..d71fc2db --- /dev/null +++ b/mixs6/me_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: ME_investigation_type + + + + +URI: [mixs.vocab:ME_investigation_type](https://w3id.org/mixs/vocab/ME_investigation_type) + + +## Domain and Range + +[ME](ME.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_lat_lon.md b/mixs6/me_lat_lon.md new file mode 100644 index 00000000..f8104a3d --- /dev/null +++ b/mixs6/me_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: ME_lat_lon + + + + +URI: [mixs.vocab:ME_lat_lon](https://w3id.org/mixs/vocab/ME_lat_lon) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_lib_layout.md b/mixs6/me_lib_layout.md new file mode 100644 index 00000000..c3107257 --- /dev/null +++ b/mixs6/me_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_layout + + + + +URI: [mixs.vocab:ME_lib_layout](https://w3id.org/mixs/vocab/ME_lib_layout) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_reads_seqd.md b/mixs6/me_lib_reads_seqd.md new file mode 100644 index 00000000..86afe779 --- /dev/null +++ b/mixs6/me_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_reads_seqd + + + + +URI: [mixs.vocab:ME_lib_reads_seqd](https://w3id.org/mixs/vocab/ME_lib_reads_seqd) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_screen.md b/mixs6/me_lib_screen.md new file mode 100644 index 00000000..a9bb47b7 --- /dev/null +++ b/mixs6/me_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_screen + + + + +URI: [mixs.vocab:ME_lib_screen](https://w3id.org/mixs/vocab/ME_lib_screen) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_size.md b/mixs6/me_lib_size.md new file mode 100644 index 00000000..2b42366a --- /dev/null +++ b/mixs6/me_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_size + + + + +URI: [mixs.vocab:ME_lib_size](https://w3id.org/mixs/vocab/ME_lib_size) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_vector.md b/mixs6/me_lib_vector.md new file mode 100644 index 00000000..c6f5a82f --- /dev/null +++ b/mixs6/me_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_vector + + + + +URI: [mixs.vocab:ME_lib_vector](https://w3id.org/mixs/vocab/ME_lib_vector) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_mid.md b/mixs6/me_mid.md new file mode 100644 index 00000000..eedad885 --- /dev/null +++ b/mixs6/me_mid.md @@ -0,0 +1,47 @@ + +# Slot: ME_mid + + + + +URI: [mixs.vocab:ME_mid](https://w3id.org/mixs/vocab/ME_mid) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_nucl_acid_amp.md b/mixs6/me_nucl_acid_amp.md new file mode 100644 index 00000000..7f3c653d --- /dev/null +++ b/mixs6/me_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: ME_nucl_acid_amp + + + + +URI: [mixs.vocab:ME_nucl_acid_amp](https://w3id.org/mixs/vocab/ME_nucl_acid_amp) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_nucl_acid_ext.md b/mixs6/me_nucl_acid_ext.md new file mode 100644 index 00000000..13c38ff6 --- /dev/null +++ b/mixs6/me_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: ME_nucl_acid_ext + + + + +URI: [mixs.vocab:ME_nucl_acid_ext](https://w3id.org/mixs/vocab/ME_nucl_acid_ext) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_number_contig.md b/mixs6/me_number_contig.md new file mode 100644 index 00000000..0d2b9f9a --- /dev/null +++ b/mixs6/me_number_contig.md @@ -0,0 +1,47 @@ + +# Slot: ME_number_contig + + + + +URI: [mixs.vocab:ME_number_contig](https://w3id.org/mixs/vocab/ME_number_contig) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_project_name.md b/mixs6/me_project_name.md new file mode 100644 index 00000000..7b988468 --- /dev/null +++ b/mixs6/me_project_name.md @@ -0,0 +1,40 @@ + +# Slot: ME_project_name + + + + +URI: [mixs.vocab:ME_project_name](https://w3id.org/mixs/vocab/ME_project_name) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_ref_biomaterial.md b/mixs6/me_ref_biomaterial.md new file mode 100644 index 00000000..a2f4f7ec --- /dev/null +++ b/mixs6/me_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: ME_ref_biomaterial + + + + +URI: [mixs.vocab:ME_ref_biomaterial](https://w3id.org/mixs/vocab/ME_ref_biomaterial) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_ref_db.md b/mixs6/me_ref_db.md new file mode 100644 index 00000000..1e279f68 --- /dev/null +++ b/mixs6/me_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: ME_ref_db + + + + +URI: [mixs.vocab:ME_ref_db](https://w3id.org/mixs/vocab/ME_ref_db) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_rel_to_oxygen.md b/mixs6/me_rel_to_oxygen.md new file mode 100644 index 00000000..c3b8e0e3 --- /dev/null +++ b/mixs6/me_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: ME_rel_to_oxygen + + + + +URI: [mixs.vocab:ME_rel_to_oxygen](https://w3id.org/mixs/vocab/ME_rel_to_oxygen) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_samp_mat_process.md b/mixs6/me_samp_mat_process.md new file mode 100644 index 00000000..fa65af01 --- /dev/null +++ b/mixs6/me_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: ME_samp_mat_process + + + + +URI: [mixs.vocab:ME_samp_mat_process](https://w3id.org/mixs/vocab/ME_samp_mat_process) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_samp_size.md b/mixs6/me_samp_size.md new file mode 100644 index 00000000..bc9b9d61 --- /dev/null +++ b/mixs6/me_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: ME_samp_size + + + + +URI: [mixs.vocab:ME_samp_size](https://w3id.org/mixs/vocab/ME_samp_size) + + +## Domain and Range + +[ME](ME.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_sample_name.md b/mixs6/me_sample_name.md new file mode 100644 index 00000000..251b038f --- /dev/null +++ b/mixs6/me_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: ME_sample_name + + + + +URI: [mixs.vocab:ME_sample_name](https://w3id.org/mixs/vocab/ME_sample_name) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_seq_meth.md b/mixs6/me_seq_meth.md new file mode 100644 index 00000000..2e1c3bdd --- /dev/null +++ b/mixs6/me_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: ME_seq_meth + + + + +URI: [mixs.vocab:ME_seq_meth](https://w3id.org/mixs/vocab/ME_seq_meth) + + +## Domain and Range + +[ME](ME.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_sim_search_meth.md b/mixs6/me_sim_search_meth.md new file mode 100644 index 00000000..a721b8a9 --- /dev/null +++ b/mixs6/me_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: ME_sim_search_meth + + + + +URI: [mixs.vocab:ME_sim_search_meth](https://w3id.org/mixs/vocab/ME_sim_search_meth) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_size_frac.md b/mixs6/me_size_frac.md new file mode 100644 index 00000000..361103e6 --- /dev/null +++ b/mixs6/me_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: ME_size_frac + + + + +URI: [mixs.vocab:ME_size_frac](https://w3id.org/mixs/vocab/ME_size_frac) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_sop.md b/mixs6/me_sop.md new file mode 100644 index 00000000..fdfe83f6 --- /dev/null +++ b/mixs6/me_sop.md @@ -0,0 +1,47 @@ + +# Slot: ME_sop + + + + +URI: [mixs.vocab:ME_sop](https://w3id.org/mixs/vocab/ME_sop) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_source_mat_id.md b/mixs6/me_source_mat_id.md new file mode 100644 index 00000000..78bcde31 --- /dev/null +++ b/mixs6/me_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: ME_source_mat_id + + + + +URI: [mixs.vocab:ME_source_mat_id](https://w3id.org/mixs/vocab/ME_source_mat_id) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_submitted_to_insdc.md b/mixs6/me_submitted_to_insdc.md new file mode 100644 index 00000000..49cf96a8 --- /dev/null +++ b/mixs6/me_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: ME_submitted_to_insdc + + + + +URI: [mixs.vocab:ME_submitted_to_insdc](https://w3id.org/mixs/vocab/ME_submitted_to_insdc) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_tax_class.md b/mixs6/me_tax_class.md new file mode 100644 index 00000000..476a0ccc --- /dev/null +++ b/mixs6/me_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: ME_tax_class + + + + +URI: [mixs.vocab:ME_tax_class](https://w3id.org/mixs/vocab/ME_tax_class) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_url.md b/mixs6/me_url.md new file mode 100644 index 00000000..9e37b8b0 --- /dev/null +++ b/mixs6/me_url.md @@ -0,0 +1,47 @@ + +# Slot: ME_url + + + + +URI: [mixs.vocab:ME_url](https://w3id.org/mixs/vocab/ME_url) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mean_frict_vel.md b/mixs6/mean_frict_vel.md new file mode 100644 index 00000000..47448218 --- /dev/null +++ b/mixs6/mean_frict_vel.md @@ -0,0 +1,72 @@ + +# Slot: mean_frict_vel + + +Measurement of mean friction velocity + +URI: [mixs.vocab:mean_frict_vel](https://w3id.org/mixs/vocab/mean_frict_vel) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean friction velocity | +| **Mappings:** | | MIXS:0000498 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter per second | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.5 meter per second', description=None) | + diff --git a/mixs6/mean_peak_frict_vel.md b/mixs6/mean_peak_frict_vel.md new file mode 100644 index 00000000..db04b786 --- /dev/null +++ b/mixs6/mean_peak_frict_vel.md @@ -0,0 +1,72 @@ + +# Slot: mean_peak_frict_vel + + +Measurement of mean peak friction velocity + +URI: [mixs.vocab:mean_peak_frict_vel](https://w3id.org/mixs/vocab/mean_peak_frict_vel) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean peak friction velocity | +| **Mappings:** | | MIXS:0000502 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter per second | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='1 meter per second', description=None) | + diff --git a/mixs6/mech_struc.md b/mixs6/mech_struc.md new file mode 100644 index 00000000..2aff3998 --- /dev/null +++ b/mixs6/mech_struc.md @@ -0,0 +1,47 @@ + +# Slot: mech_struc + + +mechanical structure: a moving structure + +URI: [mixs.vocab:mech_struc](https://w3id.org/mixs/vocab/mech_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mechanical structure | +| **Mappings:** | | MIXS:0000815 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 91.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='elevator', description=None) | + diff --git a/mixs6/mechanical_damage.md b/mixs6/mechanical_damage.md new file mode 100644 index 00000000..d8986e86 --- /dev/null +++ b/mixs6/mechanical_damage.md @@ -0,0 +1,47 @@ + +# Slot: mechanical_damage + + +Information about any mechanical damage exerted on the plant; can include multiple damages and sites + +URI: [mixs.vocab:mechanical_damage](https://w3id.org/mixs/vocab/mechanical_damage) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mechanical damage | +| **Mappings:** | | MIXS:0001052 | +| **Comments:** | | Expected value: damage type;body site | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='pruning;bark', description=None) | + diff --git a/mixs6/medic_hist_perform.md b/mixs6/medic_hist_perform.md new file mode 100644 index 00000000..c31d1b68 --- /dev/null +++ b/mixs6/medic_hist_perform.md @@ -0,0 +1,95 @@ + +# Slot: medic_hist_perform + + +Whether full medical history was collected + +URI: [mixs.vocab:medic_hist_perform](https://w3id.org/mixs/vocab/medic_hist_perform) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | medical history performed | +| **Mappings:** | | MIXS:0000897 | +| **Comments:** | | Expected value: true or false | +| | | Occurrence: 1 | +| | | Position: 28.0 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='TRUE', description=None) | + diff --git a/mixs6/menarche.md b/mixs6/menarche.md new file mode 100644 index 00000000..0b113c28 --- /dev/null +++ b/mixs6/menarche.md @@ -0,0 +1,47 @@ + +# Slot: menarche + + +Date of most recent menstruation + +URI: [mixs.vocab:menarche](https://w3id.org/mixs/vocab/menarche) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | menarche | +| **Mappings:** | | MIXS:0000965 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/menopause.md b/mixs6/menopause.md new file mode 100644 index 00000000..7aa150d6 --- /dev/null +++ b/mixs6/menopause.md @@ -0,0 +1,47 @@ + +# Slot: menopause + + +Date of onset of menopause + +URI: [mixs.vocab:menopause](https://w3id.org/mixs/vocab/menopause) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | menopause | +| **Mappings:** | | MIXS:0000968 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 6.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/methane.md b/mixs6/methane.md new file mode 100644 index 00000000..68917fb0 --- /dev/null +++ b/mixs6/methane.md @@ -0,0 +1,72 @@ + +# Slot: methane + + +Methane (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:methane](https://w3id.org/mixs/vocab/methane) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | methane | +| **Mappings:** | | MIXS:0000101 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, parts per billion, parts per million | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: air, microbial mat_biofilm, sediment | +| **Examples:** | | Example(value='1800 parts per billion', description=None) | + diff --git a/mixs6/microbial_biomass.md b/mixs6/microbial_biomass.md new file mode 100644 index 00000000..8b376cb5 --- /dev/null +++ b/mixs6/microbial_biomass.md @@ -0,0 +1,48 @@ + +# Slot: microbial_biomass + + +The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + +URI: [mixs.vocab:microbial_biomass](https://w3id.org/mixs/vocab/microbial_biomass) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | microbial biomass | +| **Mappings:** | | MIXS:0000650 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: ton, kilogram, gram per kilogram soil | +| | | Occurrence: 1 | +| | | Position: 43.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/microbial_biomass_meth.md b/mixs6/microbial_biomass_meth.md new file mode 100644 index 00000000..d3878f35 --- /dev/null +++ b/mixs6/microbial_biomass_meth.md @@ -0,0 +1,47 @@ + +# Slot: microbial_biomass_meth + + +Reference or method used in determining microbial biomass + +URI: [mixs.vocab:microbial_biomass_meth](https://w3id.org/mixs/vocab/microbial_biomass_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | microbial biomass method | +| **Mappings:** | | MIXS:0000339 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 44.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/mid.md b/mixs6/mid.md new file mode 100644 index 00000000..90b166e3 --- /dev/null +++ b/mixs6/mid.md @@ -0,0 +1,38 @@ + +# Slot: mid + + +Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + +URI: [mixs.vocab:mid](https://w3id.org/mixs/vocab/mid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞mid](ME_mid.md) + * [MIMAG➞mid](MIMAG_mid.md) + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) + * [MISAG➞mid](MISAG_mid.md) + * [MIUVIG➞mid](MIUVIG_mid.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | multiplex identifiers | +| **Comments:** | | Expected value: multiplex identifier sequence | +| | | Position: 47.0 | +| **Examples:** | | Example(value='GTGAATAT', description=None) | + diff --git a/mixs6/migs_org_adapters.md b/mixs6/migs_org_adapters.md new file mode 100644 index 00000000..a28fe001 --- /dev/null +++ b/mixs6/migs_org_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_adapters + + + + +URI: [mixs.vocab:MIGS_org_adapters](https://w3id.org/mixs/vocab/MIGS_org_adapters) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_annot.md b/mixs6/migs_org_annot.md new file mode 100644 index 00000000..3a6ec145 --- /dev/null +++ b/mixs6/migs_org_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_annot + + + + +URI: [mixs.vocab:MIGS_org_annot](https://w3id.org/mixs/vocab/MIGS_org_annot) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_assembly_name.md b/mixs6/migs_org_assembly_name.md new file mode 100644 index 00000000..7fd76fae --- /dev/null +++ b/mixs6/migs_org_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_assembly_name + + + + +URI: [mixs.vocab:MIGS_org_assembly_name](https://w3id.org/mixs/vocab/MIGS_org_assembly_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_assembly_qual.md b/mixs6/migs_org_assembly_qual.md new file mode 100644 index 00000000..6d3f890e --- /dev/null +++ b/mixs6/migs_org_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_assembly_qual + + + + +URI: [mixs.vocab:MIGS_org_assembly_qual](https://w3id.org/mixs/vocab/MIGS_org_assembly_qual) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_assembly_software.md b/mixs6/migs_org_assembly_software.md new file mode 100644 index 00000000..376e5c55 --- /dev/null +++ b/mixs6/migs_org_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_assembly_software + + + + +URI: [mixs.vocab:MIGS_org_assembly_software](https://w3id.org/mixs/vocab/MIGS_org_assembly_software) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_collection_date.md b/mixs6/migs_org_collection_date.md new file mode 100644 index 00000000..ef25e3a7 --- /dev/null +++ b/mixs6/migs_org_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_collection_date + + + + +URI: [mixs.vocab:MIGS_org_collection_date](https://w3id.org/mixs/vocab/MIGS_org_collection_date) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_compl_score.md b/mixs6/migs_org_compl_score.md new file mode 100644 index 00000000..0f839e58 --- /dev/null +++ b/mixs6/migs_org_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_compl_score + + + + +URI: [mixs.vocab:MIGS_org_compl_score](https://w3id.org/mixs/vocab/MIGS_org_compl_score) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_compl_software.md b/mixs6/migs_org_compl_software.md new file mode 100644 index 00000000..8024e1d3 --- /dev/null +++ b/mixs6/migs_org_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_compl_software + + + + +URI: [mixs.vocab:MIGS_org_compl_software](https://w3id.org/mixs/vocab/MIGS_org_compl_software) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_env_broad_scale.md b/mixs6/migs_org_env_broad_scale.md new file mode 100644 index 00000000..84a4487b --- /dev/null +++ b/mixs6/migs_org_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_org_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_org_env_broad_scale) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_env_local_scale.md b/mixs6/migs_org_env_local_scale.md new file mode 100644 index 00000000..522c0f2f --- /dev/null +++ b/mixs6/migs_org_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_env_local_scale + + + + +URI: [mixs.vocab:MIGS_org_env_local_scale](https://w3id.org/mixs/vocab/MIGS_org_env_local_scale) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_env_medium.md b/mixs6/migs_org_env_medium.md new file mode 100644 index 00000000..bd2df2e3 --- /dev/null +++ b/mixs6/migs_org_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_env_medium + + + + +URI: [mixs.vocab:MIGS_org_env_medium](https://w3id.org/mixs/vocab/MIGS_org_env_medium) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_env_package.md b/mixs6/migs_org_env_package.md new file mode 100644 index 00000000..37bce3a7 --- /dev/null +++ b/mixs6/migs_org_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_env_package + + + + +URI: [mixs.vocab:MIGS_org_env_package](https://w3id.org/mixs/vocab/MIGS_org_env_package) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_estimated_size.md b/mixs6/migs_org_estimated_size.md new file mode 100644 index 00000000..42e6877d --- /dev/null +++ b/mixs6/migs_org_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_estimated_size + + + + +URI: [mixs.vocab:MIGS_org_estimated_size](https://w3id.org/mixs/vocab/MIGS_org_estimated_size) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_experimental_factor.md b/mixs6/migs_org_experimental_factor.md new file mode 100644 index 00000000..df513b32 --- /dev/null +++ b/mixs6/migs_org_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_experimental_factor + + + + +URI: [mixs.vocab:MIGS_org_experimental_factor](https://w3id.org/mixs/vocab/MIGS_org_experimental_factor) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_extrachrom_elements.md b/mixs6/migs_org_extrachrom_elements.md new file mode 100644 index 00000000..c3c07183 --- /dev/null +++ b/mixs6/migs_org_extrachrom_elements.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_extrachrom_elements + + + + +URI: [mixs.vocab:MIGS_org_extrachrom_elements](https://w3id.org/mixs/vocab/MIGS_org_extrachrom_elements) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_feat_pred.md b/mixs6/migs_org_feat_pred.md new file mode 100644 index 00000000..3c781cff --- /dev/null +++ b/mixs6/migs_org_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_feat_pred + + + + +URI: [mixs.vocab:MIGS_org_feat_pred](https://w3id.org/mixs/vocab/MIGS_org_feat_pred) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_geo_loc_name.md b/mixs6/migs_org_geo_loc_name.md new file mode 100644 index 00000000..dc43148f --- /dev/null +++ b/mixs6/migs_org_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_org_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_org_geo_loc_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_investigation_type.md b/mixs6/migs_org_investigation_type.md new file mode 100644 index 00000000..e70b04be --- /dev/null +++ b/mixs6/migs_org_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_investigation_type + + + + +URI: [mixs.vocab:MIGS_org_investigation_type](https://w3id.org/mixs/vocab/MIGS_org_investigation_type) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_isol_growth_condt.md b/mixs6/migs_org_isol_growth_condt.md new file mode 100644 index 00000000..aa130ab9 --- /dev/null +++ b/mixs6/migs_org_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_org_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_org_isol_growth_condt) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lat_lon.md b/mixs6/migs_org_lat_lon.md new file mode 100644 index 00000000..cfad477f --- /dev/null +++ b/mixs6/migs_org_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_lat_lon + + + + +URI: [mixs.vocab:MIGS_org_lat_lon](https://w3id.org/mixs/vocab/MIGS_org_lat_lon) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_lib_layout.md b/mixs6/migs_org_lib_layout.md new file mode 100644 index 00000000..5030e4e2 --- /dev/null +++ b/mixs6/migs_org_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_layout + + + + +URI: [mixs.vocab:MIGS_org_lib_layout](https://w3id.org/mixs/vocab/MIGS_org_lib_layout) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_reads_seqd.md b/mixs6/migs_org_lib_reads_seqd.md new file mode 100644 index 00000000..2297ac3b --- /dev/null +++ b/mixs6/migs_org_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_org_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_org_lib_reads_seqd) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_screen.md b/mixs6/migs_org_lib_screen.md new file mode 100644 index 00000000..e0d119a0 --- /dev/null +++ b/mixs6/migs_org_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_screen + + + + +URI: [mixs.vocab:MIGS_org_lib_screen](https://w3id.org/mixs/vocab/MIGS_org_lib_screen) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_size.md b/mixs6/migs_org_lib_size.md new file mode 100644 index 00000000..67f1bdc9 --- /dev/null +++ b/mixs6/migs_org_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_size + + + + +URI: [mixs.vocab:MIGS_org_lib_size](https://w3id.org/mixs/vocab/MIGS_org_lib_size) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_vector.md b/mixs6/migs_org_lib_vector.md new file mode 100644 index 00000000..f0bacaf9 --- /dev/null +++ b/mixs6/migs_org_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_vector + + + + +URI: [mixs.vocab:MIGS_org_lib_vector](https://w3id.org/mixs/vocab/MIGS_org_lib_vector) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_nucl_acid_amp.md b/mixs6/migs_org_nucl_acid_amp.md new file mode 100644 index 00000000..c8043784 --- /dev/null +++ b/mixs6/migs_org_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_org_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_org_nucl_acid_amp) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_nucl_acid_ext.md b/mixs6/migs_org_nucl_acid_ext.md new file mode 100644 index 00000000..b429d808 --- /dev/null +++ b/mixs6/migs_org_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_org_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_org_nucl_acid_ext) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_number_contig.md b/mixs6/migs_org_number_contig.md new file mode 100644 index 00000000..57f35064 --- /dev/null +++ b/mixs6/migs_org_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_number_contig + + + + +URI: [mixs.vocab:MIGS_org_number_contig](https://w3id.org/mixs/vocab/MIGS_org_number_contig) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_project_name.md b/mixs6/migs_org_project_name.md new file mode 100644 index 00000000..9fa9c971 --- /dev/null +++ b/mixs6/migs_org_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_project_name + + + + +URI: [mixs.vocab:MIGS_org_project_name](https://w3id.org/mixs/vocab/MIGS_org_project_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_ref_biomaterial.md b/mixs6/migs_org_ref_biomaterial.md new file mode 100644 index 00000000..1d5e8643 --- /dev/null +++ b/mixs6/migs_org_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_org_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_org_ref_biomaterial) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_ref_db.md b/mixs6/migs_org_ref_db.md new file mode 100644 index 00000000..1c94ff68 --- /dev/null +++ b/mixs6/migs_org_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_ref_db + + + + +URI: [mixs.vocab:MIGS_org_ref_db](https://w3id.org/mixs/vocab/MIGS_org_ref_db) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_samp_mat_process.md b/mixs6/migs_org_samp_mat_process.md new file mode 100644 index 00000000..ed21c591 --- /dev/null +++ b/mixs6/migs_org_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_org_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_org_samp_mat_process) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_samp_size.md b/mixs6/migs_org_samp_size.md new file mode 100644 index 00000000..140213d8 --- /dev/null +++ b/mixs6/migs_org_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_samp_size + + + + +URI: [mixs.vocab:MIGS_org_samp_size](https://w3id.org/mixs/vocab/MIGS_org_samp_size) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_sample_name.md b/mixs6/migs_org_sample_name.md new file mode 100644 index 00000000..d4e3f0c3 --- /dev/null +++ b/mixs6/migs_org_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_sample_name + + + + +URI: [mixs.vocab:MIGS_org_sample_name](https://w3id.org/mixs/vocab/MIGS_org_sample_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_seq_meth.md b/mixs6/migs_org_seq_meth.md new file mode 100644 index 00000000..c242cfa6 --- /dev/null +++ b/mixs6/migs_org_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_seq_meth + + + + +URI: [mixs.vocab:MIGS_org_seq_meth](https://w3id.org/mixs/vocab/MIGS_org_seq_meth) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_sim_search_meth.md b/mixs6/migs_org_sim_search_meth.md new file mode 100644 index 00000000..c7853eaf --- /dev/null +++ b/mixs6/migs_org_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_org_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_org_sim_search_meth) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_sop.md b/mixs6/migs_org_sop.md new file mode 100644 index 00000000..e34c6f3b --- /dev/null +++ b/mixs6/migs_org_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_sop + + + + +URI: [mixs.vocab:MIGS_org_sop](https://w3id.org/mixs/vocab/MIGS_org_sop) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_source_mat_id.md b/mixs6/migs_org_source_mat_id.md new file mode 100644 index 00000000..343e9cc8 --- /dev/null +++ b/mixs6/migs_org_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_source_mat_id + + + + +URI: [mixs.vocab:MIGS_org_source_mat_id](https://w3id.org/mixs/vocab/MIGS_org_source_mat_id) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_submitted_to_insdc.md b/mixs6/migs_org_submitted_to_insdc.md new file mode 100644 index 00000000..29531604 --- /dev/null +++ b/mixs6/migs_org_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_org_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_org_submitted_to_insdc) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_subspecf_gen_lin.md b/mixs6/migs_org_subspecf_gen_lin.md new file mode 100644 index 00000000..2602a635 --- /dev/null +++ b/mixs6/migs_org_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_org_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_org_subspecf_gen_lin) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_tax_class.md b/mixs6/migs_org_tax_class.md new file mode 100644 index 00000000..470eac16 --- /dev/null +++ b/mixs6/migs_org_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_tax_class + + + + +URI: [mixs.vocab:MIGS_org_tax_class](https://w3id.org/mixs/vocab/MIGS_org_tax_class) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_tax_ident.md b/mixs6/migs_org_tax_ident.md new file mode 100644 index 00000000..d49592dd --- /dev/null +++ b/mixs6/migs_org_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_tax_ident + + + + +URI: [mixs.vocab:MIGS_org_tax_ident](https://w3id.org/mixs/vocab/MIGS_org_tax_ident) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_url.md b/mixs6/migs_org_url.md new file mode 100644 index 00000000..c8e99c2c --- /dev/null +++ b/mixs6/migs_org_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_url + + + + +URI: [mixs.vocab:MIGS_org_url](https://w3id.org/mixs/vocab/MIGS_org_url) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_adapters.md b/mixs6/mimag_adapters.md new file mode 100644 index 00000000..d90e0432 --- /dev/null +++ b/mixs6/mimag_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_adapters + + + + +URI: [mixs.vocab:MIMAG_adapters](https://w3id.org/mixs/vocab/MIMAG_adapters) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_annot.md b/mixs6/mimag_annot.md new file mode 100644 index 00000000..8624758f --- /dev/null +++ b/mixs6/mimag_annot.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_annot + + + + +URI: [mixs.vocab:MIMAG_annot](https://w3id.org/mixs/vocab/MIMAG_annot) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_assembly_name.md b/mixs6/mimag_assembly_name.md new file mode 100644 index 00000000..8edc97de --- /dev/null +++ b/mixs6/mimag_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_assembly_name + + + + +URI: [mixs.vocab:MIMAG_assembly_name](https://w3id.org/mixs/vocab/MIMAG_assembly_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_assembly_qual.md b/mixs6/mimag_assembly_qual.md new file mode 100644 index 00000000..274945a1 --- /dev/null +++ b/mixs6/mimag_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_assembly_qual + + + + +URI: [mixs.vocab:MIMAG_assembly_qual](https://w3id.org/mixs/vocab/MIMAG_assembly_qual) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_assembly_software.md b/mixs6/mimag_assembly_software.md new file mode 100644 index 00000000..2d3f8b61 --- /dev/null +++ b/mixs6/mimag_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_assembly_software + + + + +URI: [mixs.vocab:MIMAG_assembly_software](https://w3id.org/mixs/vocab/MIMAG_assembly_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_bin_param.md b/mixs6/mimag_bin_param.md new file mode 100644 index 00000000..ee267096 --- /dev/null +++ b/mixs6/mimag_bin_param.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_bin_param + + + + +URI: [mixs.vocab:MIMAG_bin_param](https://w3id.org/mixs/vocab/MIMAG_bin_param) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [bin_param](bin_param.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_bin_software.md b/mixs6/mimag_bin_software.md new file mode 100644 index 00000000..d72ad7be --- /dev/null +++ b/mixs6/mimag_bin_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_bin_software + + + + +URI: [mixs.vocab:MIMAG_bin_software](https://w3id.org/mixs/vocab/MIMAG_bin_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [bin_software](bin_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_collection_date.md b/mixs6/mimag_collection_date.md new file mode 100644 index 00000000..6aaedfb9 --- /dev/null +++ b/mixs6/mimag_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_collection_date + + + + +URI: [mixs.vocab:MIMAG_collection_date](https://w3id.org/mixs/vocab/MIMAG_collection_date) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_compl_appr.md b/mixs6/mimag_compl_appr.md new file mode 100644 index 00000000..cdf87307 --- /dev/null +++ b/mixs6/mimag_compl_appr.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_compl_appr + + + + +URI: [mixs.vocab:MIMAG_compl_appr](https://w3id.org/mixs/vocab/MIMAG_compl_appr) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [compl_appr](compl_appr.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_compl_score.md b/mixs6/mimag_compl_score.md new file mode 100644 index 00000000..6faad65d --- /dev/null +++ b/mixs6/mimag_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_compl_score + + + + +URI: [mixs.vocab:MIMAG_compl_score](https://w3id.org/mixs/vocab/MIMAG_compl_score) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_compl_software.md b/mixs6/mimag_compl_software.md new file mode 100644 index 00000000..4f7ef72b --- /dev/null +++ b/mixs6/mimag_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_compl_software + + + + +URI: [mixs.vocab:MIMAG_compl_software](https://w3id.org/mixs/vocab/MIMAG_compl_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_contam_score.md b/mixs6/mimag_contam_score.md new file mode 100644 index 00000000..f6e043e5 --- /dev/null +++ b/mixs6/mimag_contam_score.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_contam_score + + + + +URI: [mixs.vocab:MIMAG_contam_score](https://w3id.org/mixs/vocab/MIMAG_contam_score) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [contam_score](contam_score.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_contam_screen_input.md b/mixs6/mimag_contam_screen_input.md new file mode 100644 index 00000000..2ae01980 --- /dev/null +++ b/mixs6/mimag_contam_screen_input.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_contam_screen_input + + + + +URI: [mixs.vocab:MIMAG_contam_screen_input](https://w3id.org/mixs/vocab/MIMAG_contam_screen_input) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [contam_screen_input](contam_screen_input.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_contam_screen_param.md b/mixs6/mimag_contam_screen_param.md new file mode 100644 index 00000000..5ff87855 --- /dev/null +++ b/mixs6/mimag_contam_screen_param.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_contam_screen_param + + + + +URI: [mixs.vocab:MIMAG_contam_screen_param](https://w3id.org/mixs/vocab/MIMAG_contam_screen_param) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [contam_screen_param](contam_screen_param.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_decontam_software.md b/mixs6/mimag_decontam_software.md new file mode 100644 index 00000000..b94187ce --- /dev/null +++ b/mixs6/mimag_decontam_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_decontam_software + + + + +URI: [mixs.vocab:MIMAG_decontam_software](https://w3id.org/mixs/vocab/MIMAG_decontam_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [decontam_software](decontam_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_env_broad_scale.md b/mixs6/mimag_env_broad_scale.md new file mode 100644 index 00000000..91939812 --- /dev/null +++ b/mixs6/mimag_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_env_broad_scale + + + + +URI: [mixs.vocab:MIMAG_env_broad_scale](https://w3id.org/mixs/vocab/MIMAG_env_broad_scale) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_env_local_scale.md b/mixs6/mimag_env_local_scale.md new file mode 100644 index 00000000..80017ddc --- /dev/null +++ b/mixs6/mimag_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_env_local_scale + + + + +URI: [mixs.vocab:MIMAG_env_local_scale](https://w3id.org/mixs/vocab/MIMAG_env_local_scale) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_env_medium.md b/mixs6/mimag_env_medium.md new file mode 100644 index 00000000..13770f6a --- /dev/null +++ b/mixs6/mimag_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_env_medium + + + + +URI: [mixs.vocab:MIMAG_env_medium](https://w3id.org/mixs/vocab/MIMAG_env_medium) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_env_package.md b/mixs6/mimag_env_package.md new file mode 100644 index 00000000..8e7d6506 --- /dev/null +++ b/mixs6/mimag_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_env_package + + + + +URI: [mixs.vocab:MIMAG_env_package](https://w3id.org/mixs/vocab/MIMAG_env_package) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_experimental_factor.md b/mixs6/mimag_experimental_factor.md new file mode 100644 index 00000000..58c230d9 --- /dev/null +++ b/mixs6/mimag_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_experimental_factor + + + + +URI: [mixs.vocab:MIMAG_experimental_factor](https://w3id.org/mixs/vocab/MIMAG_experimental_factor) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_feat_pred.md b/mixs6/mimag_feat_pred.md new file mode 100644 index 00000000..ab41ee9c --- /dev/null +++ b/mixs6/mimag_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_feat_pred + + + + +URI: [mixs.vocab:MIMAG_feat_pred](https://w3id.org/mixs/vocab/MIMAG_feat_pred) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_geo_loc_name.md b/mixs6/mimag_geo_loc_name.md new file mode 100644 index 00000000..690a20c6 --- /dev/null +++ b/mixs6/mimag_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_geo_loc_name + + + + +URI: [mixs.vocab:MIMAG_geo_loc_name](https://w3id.org/mixs/vocab/MIMAG_geo_loc_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_investigation_type.md b/mixs6/mimag_investigation_type.md new file mode 100644 index 00000000..0cb1b3f6 --- /dev/null +++ b/mixs6/mimag_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_investigation_type + + + + +URI: [mixs.vocab:MIMAG_investigation_type](https://w3id.org/mixs/vocab/MIMAG_investigation_type) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_lat_lon.md b/mixs6/mimag_lat_lon.md new file mode 100644 index 00000000..97658751 --- /dev/null +++ b/mixs6/mimag_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_lat_lon + + + + +URI: [mixs.vocab:MIMAG_lat_lon](https://w3id.org/mixs/vocab/MIMAG_lat_lon) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_lib_layout.md b/mixs6/mimag_lib_layout.md new file mode 100644 index 00000000..44e094cc --- /dev/null +++ b/mixs6/mimag_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_layout + + + + +URI: [mixs.vocab:MIMAG_lib_layout](https://w3id.org/mixs/vocab/MIMAG_lib_layout) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_reads_seqd.md b/mixs6/mimag_lib_reads_seqd.md new file mode 100644 index 00000000..88d873ce --- /dev/null +++ b/mixs6/mimag_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_reads_seqd + + + + +URI: [mixs.vocab:MIMAG_lib_reads_seqd](https://w3id.org/mixs/vocab/MIMAG_lib_reads_seqd) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_screen.md b/mixs6/mimag_lib_screen.md new file mode 100644 index 00000000..4ffa0d3d --- /dev/null +++ b/mixs6/mimag_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_screen + + + + +URI: [mixs.vocab:MIMAG_lib_screen](https://w3id.org/mixs/vocab/MIMAG_lib_screen) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_size.md b/mixs6/mimag_lib_size.md new file mode 100644 index 00000000..1f42fc15 --- /dev/null +++ b/mixs6/mimag_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_size + + + + +URI: [mixs.vocab:MIMAG_lib_size](https://w3id.org/mixs/vocab/MIMAG_lib_size) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_vector.md b/mixs6/mimag_lib_vector.md new file mode 100644 index 00000000..58c1635a --- /dev/null +++ b/mixs6/mimag_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_vector + + + + +URI: [mixs.vocab:MIMAG_lib_vector](https://w3id.org/mixs/vocab/MIMAG_lib_vector) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_mag_cov_software.md b/mixs6/mimag_mag_cov_software.md new file mode 100644 index 00000000..6ddb533a --- /dev/null +++ b/mixs6/mimag_mag_cov_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_mag_cov_software + + + + +URI: [mixs.vocab:MIMAG_mag_cov_software](https://w3id.org/mixs/vocab/MIMAG_mag_cov_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [mag_cov_software](mag_cov_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_mid.md b/mixs6/mimag_mid.md new file mode 100644 index 00000000..4c92bcec --- /dev/null +++ b/mixs6/mimag_mid.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_mid + + + + +URI: [mixs.vocab:MIMAG_mid](https://w3id.org/mixs/vocab/MIMAG_mid) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_nucl_acid_amp.md b/mixs6/mimag_nucl_acid_amp.md new file mode 100644 index 00000000..56cde0a8 --- /dev/null +++ b/mixs6/mimag_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_nucl_acid_amp + + + + +URI: [mixs.vocab:MIMAG_nucl_acid_amp](https://w3id.org/mixs/vocab/MIMAG_nucl_acid_amp) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_nucl_acid_ext.md b/mixs6/mimag_nucl_acid_ext.md new file mode 100644 index 00000000..ef861b55 --- /dev/null +++ b/mixs6/mimag_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_nucl_acid_ext + + + + +URI: [mixs.vocab:MIMAG_nucl_acid_ext](https://w3id.org/mixs/vocab/MIMAG_nucl_acid_ext) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_number_contig.md b/mixs6/mimag_number_contig.md new file mode 100644 index 00000000..fd13378b --- /dev/null +++ b/mixs6/mimag_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_number_contig + + + + +URI: [mixs.vocab:MIMAG_number_contig](https://w3id.org/mixs/vocab/MIMAG_number_contig) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_project_name.md b/mixs6/mimag_project_name.md new file mode 100644 index 00000000..291c914e --- /dev/null +++ b/mixs6/mimag_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_project_name + + + + +URI: [mixs.vocab:MIMAG_project_name](https://w3id.org/mixs/vocab/MIMAG_project_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_reassembly_bin.md b/mixs6/mimag_reassembly_bin.md new file mode 100644 index 00000000..4191fc58 --- /dev/null +++ b/mixs6/mimag_reassembly_bin.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_reassembly_bin + + + + +URI: [mixs.vocab:MIMAG_reassembly_bin](https://w3id.org/mixs/vocab/MIMAG_reassembly_bin) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [reassembly_bin](reassembly_bin.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_ref_biomaterial.md b/mixs6/mimag_ref_biomaterial.md new file mode 100644 index 00000000..0468abf3 --- /dev/null +++ b/mixs6/mimag_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_ref_biomaterial + + + + +URI: [mixs.vocab:MIMAG_ref_biomaterial](https://w3id.org/mixs/vocab/MIMAG_ref_biomaterial) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_ref_db.md b/mixs6/mimag_ref_db.md new file mode 100644 index 00000000..c4c48b1e --- /dev/null +++ b/mixs6/mimag_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_ref_db + + + + +URI: [mixs.vocab:MIMAG_ref_db](https://w3id.org/mixs/vocab/MIMAG_ref_db) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_rel_to_oxygen.md b/mixs6/mimag_rel_to_oxygen.md new file mode 100644 index 00000000..3d4cf051 --- /dev/null +++ b/mixs6/mimag_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_rel_to_oxygen + + + + +URI: [mixs.vocab:MIMAG_rel_to_oxygen](https://w3id.org/mixs/vocab/MIMAG_rel_to_oxygen) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_samp_mat_process.md b/mixs6/mimag_samp_mat_process.md new file mode 100644 index 00000000..a758e129 --- /dev/null +++ b/mixs6/mimag_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_samp_mat_process + + + + +URI: [mixs.vocab:MIMAG_samp_mat_process](https://w3id.org/mixs/vocab/MIMAG_samp_mat_process) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_samp_size.md b/mixs6/mimag_samp_size.md new file mode 100644 index 00000000..2adf058f --- /dev/null +++ b/mixs6/mimag_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_samp_size + + + + +URI: [mixs.vocab:MIMAG_samp_size](https://w3id.org/mixs/vocab/MIMAG_samp_size) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_sample_name.md b/mixs6/mimag_sample_name.md new file mode 100644 index 00000000..a150cce3 --- /dev/null +++ b/mixs6/mimag_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_sample_name + + + + +URI: [mixs.vocab:MIMAG_sample_name](https://w3id.org/mixs/vocab/MIMAG_sample_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_seq_meth.md b/mixs6/mimag_seq_meth.md new file mode 100644 index 00000000..ec64f504 --- /dev/null +++ b/mixs6/mimag_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_seq_meth + + + + +URI: [mixs.vocab:MIMAG_seq_meth](https://w3id.org/mixs/vocab/MIMAG_seq_meth) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_sim_search_meth.md b/mixs6/mimag_sim_search_meth.md new file mode 100644 index 00000000..5be7e7fb --- /dev/null +++ b/mixs6/mimag_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_sim_search_meth + + + + +URI: [mixs.vocab:MIMAG_sim_search_meth](https://w3id.org/mixs/vocab/MIMAG_sim_search_meth) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_size_frac.md b/mixs6/mimag_size_frac.md new file mode 100644 index 00000000..0c8fcd9f --- /dev/null +++ b/mixs6/mimag_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_size_frac + + + + +URI: [mixs.vocab:MIMAG_size_frac](https://w3id.org/mixs/vocab/MIMAG_size_frac) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_sop.md b/mixs6/mimag_sop.md new file mode 100644 index 00000000..0ae6cf9f --- /dev/null +++ b/mixs6/mimag_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_sop + + + + +URI: [mixs.vocab:MIMAG_sop](https://w3id.org/mixs/vocab/MIMAG_sop) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_source_mat_id.md b/mixs6/mimag_source_mat_id.md new file mode 100644 index 00000000..790c66f4 --- /dev/null +++ b/mixs6/mimag_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_source_mat_id + + + + +URI: [mixs.vocab:MIMAG_source_mat_id](https://w3id.org/mixs/vocab/MIMAG_source_mat_id) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_submitted_to_insdc.md b/mixs6/mimag_submitted_to_insdc.md new file mode 100644 index 00000000..5836d4df --- /dev/null +++ b/mixs6/mimag_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_submitted_to_insdc + + + + +URI: [mixs.vocab:MIMAG_submitted_to_insdc](https://w3id.org/mixs/vocab/MIMAG_submitted_to_insdc) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_tax_class.md b/mixs6/mimag_tax_class.md new file mode 100644 index 00000000..41614da2 --- /dev/null +++ b/mixs6/mimag_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_tax_class + + + + +URI: [mixs.vocab:MIMAG_tax_class](https://w3id.org/mixs/vocab/MIMAG_tax_class) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_tax_ident.md b/mixs6/mimag_tax_ident.md new file mode 100644 index 00000000..c7c8aafc --- /dev/null +++ b/mixs6/mimag_tax_ident.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_tax_ident + + + + +URI: [mixs.vocab:MIMAG_tax_ident](https://w3id.org/mixs/vocab/MIMAG_tax_ident) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_trna_ext_software.md b/mixs6/mimag_trna_ext_software.md new file mode 100644 index 00000000..0e27d2f6 --- /dev/null +++ b/mixs6/mimag_trna_ext_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_trna_ext_software + + + + +URI: [mixs.vocab:MIMAG_trna_ext_software](https://w3id.org/mixs/vocab/MIMAG_trna_ext_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trna_ext_software](trna_ext_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_trnas.md b/mixs6/mimag_trnas.md new file mode 100644 index 00000000..1a83a531 --- /dev/null +++ b/mixs6/mimag_trnas.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_trnas + + + + +URI: [mixs.vocab:MIMAG_trnas](https://w3id.org/mixs/vocab/MIMAG_trnas) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trnas](trnas.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_url.md b/mixs6/mimag_url.md new file mode 100644 index 00000000..6e717ccd --- /dev/null +++ b/mixs6/mimag_url.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_url + + + + +URI: [mixs.vocab:MIMAG_url](https://w3id.org/mixs/vocab/MIMAG_url) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_x_16s_recover.md b/mixs6/mimag_x_16s_recover.md new file mode 100644 index 00000000..59935b76 --- /dev/null +++ b/mixs6/mimag_x_16s_recover.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_x_16s_recover + + + + +URI: [mixs.vocab:MIMAG_x_16s_recover](https://w3id.org/mixs/vocab/MIMAG_x_16s_recover) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [x_16s_recover](x_16s_recover.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mineral_nutr_regm.md b/mixs6/mineral_nutr_regm.md new file mode 100644 index 00000000..d3469384 --- /dev/null +++ b/mixs6/mineral_nutr_regm.md @@ -0,0 +1,48 @@ + +# Slot: mineral_nutr_regm + + +Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + +URI: [mixs.vocab:mineral_nutr_regm](https://w3id.org/mixs/vocab/mineral_nutr_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mineral nutrient regimen | +| **Mappings:** | | MIXS:0000570 | +| **Comments:** | | Expected value: mineral nutrient name;mineral nutrient amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/misag_adapters.md b/mixs6/misag_adapters.md new file mode 100644 index 00000000..a114706c --- /dev/null +++ b/mixs6/misag_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_adapters + + + + +URI: [mixs.vocab:MISAG_adapters](https://w3id.org/mixs/vocab/MISAG_adapters) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_annot.md b/mixs6/misag_annot.md new file mode 100644 index 00000000..605703b6 --- /dev/null +++ b/mixs6/misag_annot.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_annot + + + + +URI: [mixs.vocab:MISAG_annot](https://w3id.org/mixs/vocab/MISAG_annot) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_assembly_name.md b/mixs6/misag_assembly_name.md new file mode 100644 index 00000000..cec5c3c9 --- /dev/null +++ b/mixs6/misag_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_assembly_name + + + + +URI: [mixs.vocab:MISAG_assembly_name](https://w3id.org/mixs/vocab/MISAG_assembly_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_assembly_qual.md b/mixs6/misag_assembly_qual.md new file mode 100644 index 00000000..3096c276 --- /dev/null +++ b/mixs6/misag_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_assembly_qual + + + + +URI: [mixs.vocab:MISAG_assembly_qual](https://w3id.org/mixs/vocab/MISAG_assembly_qual) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_assembly_software.md b/mixs6/misag_assembly_software.md new file mode 100644 index 00000000..a4b4d6b0 --- /dev/null +++ b/mixs6/misag_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_assembly_software + + + + +URI: [mixs.vocab:MISAG_assembly_software](https://w3id.org/mixs/vocab/MISAG_assembly_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_collection_date.md b/mixs6/misag_collection_date.md new file mode 100644 index 00000000..d0b7a5ed --- /dev/null +++ b/mixs6/misag_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_collection_date + + + + +URI: [mixs.vocab:MISAG_collection_date](https://w3id.org/mixs/vocab/MISAG_collection_date) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_compl_appr.md b/mixs6/misag_compl_appr.md new file mode 100644 index 00000000..3ed7eb42 --- /dev/null +++ b/mixs6/misag_compl_appr.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_compl_appr + + + + +URI: [mixs.vocab:MISAG_compl_appr](https://w3id.org/mixs/vocab/MISAG_compl_appr) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [compl_appr](compl_appr.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_compl_score.md b/mixs6/misag_compl_score.md new file mode 100644 index 00000000..6eb075c3 --- /dev/null +++ b/mixs6/misag_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_compl_score + + + + +URI: [mixs.vocab:MISAG_compl_score](https://w3id.org/mixs/vocab/MISAG_compl_score) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_compl_software.md b/mixs6/misag_compl_software.md new file mode 100644 index 00000000..8a733c86 --- /dev/null +++ b/mixs6/misag_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_compl_software + + + + +URI: [mixs.vocab:MISAG_compl_software](https://w3id.org/mixs/vocab/MISAG_compl_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_contam_score.md b/mixs6/misag_contam_score.md new file mode 100644 index 00000000..1b54e765 --- /dev/null +++ b/mixs6/misag_contam_score.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_contam_score + + + + +URI: [mixs.vocab:MISAG_contam_score](https://w3id.org/mixs/vocab/MISAG_contam_score) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [contam_score](contam_score.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_contam_screen_input.md b/mixs6/misag_contam_screen_input.md new file mode 100644 index 00000000..d881d54f --- /dev/null +++ b/mixs6/misag_contam_screen_input.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_contam_screen_input + + + + +URI: [mixs.vocab:MISAG_contam_screen_input](https://w3id.org/mixs/vocab/MISAG_contam_screen_input) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [contam_screen_input](contam_screen_input.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_contam_screen_param.md b/mixs6/misag_contam_screen_param.md new file mode 100644 index 00000000..458fcaa0 --- /dev/null +++ b/mixs6/misag_contam_screen_param.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_contam_screen_param + + + + +URI: [mixs.vocab:MISAG_contam_screen_param](https://w3id.org/mixs/vocab/MISAG_contam_screen_param) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [contam_screen_param](contam_screen_param.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_decontam_software.md b/mixs6/misag_decontam_software.md new file mode 100644 index 00000000..f2b95321 --- /dev/null +++ b/mixs6/misag_decontam_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_decontam_software + + + + +URI: [mixs.vocab:MISAG_decontam_software](https://w3id.org/mixs/vocab/MISAG_decontam_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [decontam_software](decontam_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_env_broad_scale.md b/mixs6/misag_env_broad_scale.md new file mode 100644 index 00000000..8cb25b24 --- /dev/null +++ b/mixs6/misag_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_env_broad_scale + + + + +URI: [mixs.vocab:MISAG_env_broad_scale](https://w3id.org/mixs/vocab/MISAG_env_broad_scale) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_env_local_scale.md b/mixs6/misag_env_local_scale.md new file mode 100644 index 00000000..205dd0be --- /dev/null +++ b/mixs6/misag_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_env_local_scale + + + + +URI: [mixs.vocab:MISAG_env_local_scale](https://w3id.org/mixs/vocab/MISAG_env_local_scale) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_env_medium.md b/mixs6/misag_env_medium.md new file mode 100644 index 00000000..2a43dec0 --- /dev/null +++ b/mixs6/misag_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_env_medium + + + + +URI: [mixs.vocab:MISAG_env_medium](https://w3id.org/mixs/vocab/MISAG_env_medium) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_env_package.md b/mixs6/misag_env_package.md new file mode 100644 index 00000000..438c6411 --- /dev/null +++ b/mixs6/misag_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_env_package + + + + +URI: [mixs.vocab:MISAG_env_package](https://w3id.org/mixs/vocab/MISAG_env_package) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_experimental_factor.md b/mixs6/misag_experimental_factor.md new file mode 100644 index 00000000..2f381967 --- /dev/null +++ b/mixs6/misag_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_experimental_factor + + + + +URI: [mixs.vocab:MISAG_experimental_factor](https://w3id.org/mixs/vocab/MISAG_experimental_factor) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_feat_pred.md b/mixs6/misag_feat_pred.md new file mode 100644 index 00000000..c263d715 --- /dev/null +++ b/mixs6/misag_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_feat_pred + + + + +URI: [mixs.vocab:MISAG_feat_pred](https://w3id.org/mixs/vocab/MISAG_feat_pred) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_geo_loc_name.md b/mixs6/misag_geo_loc_name.md new file mode 100644 index 00000000..48afa724 --- /dev/null +++ b/mixs6/misag_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_geo_loc_name + + + + +URI: [mixs.vocab:MISAG_geo_loc_name](https://w3id.org/mixs/vocab/MISAG_geo_loc_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_investigation_type.md b/mixs6/misag_investigation_type.md new file mode 100644 index 00000000..a06228f2 --- /dev/null +++ b/mixs6/misag_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_investigation_type + + + + +URI: [mixs.vocab:MISAG_investigation_type](https://w3id.org/mixs/vocab/MISAG_investigation_type) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_lat_lon.md b/mixs6/misag_lat_lon.md new file mode 100644 index 00000000..0d425b05 --- /dev/null +++ b/mixs6/misag_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_lat_lon + + + + +URI: [mixs.vocab:MISAG_lat_lon](https://w3id.org/mixs/vocab/MISAG_lat_lon) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_lib_layout.md b/mixs6/misag_lib_layout.md new file mode 100644 index 00000000..96ba5f9d --- /dev/null +++ b/mixs6/misag_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_layout + + + + +URI: [mixs.vocab:MISAG_lib_layout](https://w3id.org/mixs/vocab/MISAG_lib_layout) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_reads_seqd.md b/mixs6/misag_lib_reads_seqd.md new file mode 100644 index 00000000..2ee70bb6 --- /dev/null +++ b/mixs6/misag_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_reads_seqd + + + + +URI: [mixs.vocab:MISAG_lib_reads_seqd](https://w3id.org/mixs/vocab/MISAG_lib_reads_seqd) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_screen.md b/mixs6/misag_lib_screen.md new file mode 100644 index 00000000..9b65f378 --- /dev/null +++ b/mixs6/misag_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_screen + + + + +URI: [mixs.vocab:MISAG_lib_screen](https://w3id.org/mixs/vocab/MISAG_lib_screen) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_size.md b/mixs6/misag_lib_size.md new file mode 100644 index 00000000..93f242bc --- /dev/null +++ b/mixs6/misag_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_size + + + + +URI: [mixs.vocab:MISAG_lib_size](https://w3id.org/mixs/vocab/MISAG_lib_size) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_vector.md b/mixs6/misag_lib_vector.md new file mode 100644 index 00000000..273f09f4 --- /dev/null +++ b/mixs6/misag_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_vector + + + + +URI: [mixs.vocab:MISAG_lib_vector](https://w3id.org/mixs/vocab/MISAG_lib_vector) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_mid.md b/mixs6/misag_mid.md new file mode 100644 index 00000000..e279d26c --- /dev/null +++ b/mixs6/misag_mid.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_mid + + + + +URI: [mixs.vocab:MISAG_mid](https://w3id.org/mixs/vocab/MISAG_mid) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_nucl_acid_amp.md b/mixs6/misag_nucl_acid_amp.md new file mode 100644 index 00000000..c1ff35b3 --- /dev/null +++ b/mixs6/misag_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_nucl_acid_amp + + + + +URI: [mixs.vocab:MISAG_nucl_acid_amp](https://w3id.org/mixs/vocab/MISAG_nucl_acid_amp) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_nucl_acid_ext.md b/mixs6/misag_nucl_acid_ext.md new file mode 100644 index 00000000..cc15c052 --- /dev/null +++ b/mixs6/misag_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_nucl_acid_ext + + + + +URI: [mixs.vocab:MISAG_nucl_acid_ext](https://w3id.org/mixs/vocab/MISAG_nucl_acid_ext) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_number_contig.md b/mixs6/misag_number_contig.md new file mode 100644 index 00000000..2389dc85 --- /dev/null +++ b/mixs6/misag_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_number_contig + + + + +URI: [mixs.vocab:MISAG_number_contig](https://w3id.org/mixs/vocab/MISAG_number_contig) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_project_name.md b/mixs6/misag_project_name.md new file mode 100644 index 00000000..943c0c55 --- /dev/null +++ b/mixs6/misag_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_project_name + + + + +URI: [mixs.vocab:MISAG_project_name](https://w3id.org/mixs/vocab/MISAG_project_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_ref_biomaterial.md b/mixs6/misag_ref_biomaterial.md new file mode 100644 index 00000000..6bb610b2 --- /dev/null +++ b/mixs6/misag_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_ref_biomaterial + + + + +URI: [mixs.vocab:MISAG_ref_biomaterial](https://w3id.org/mixs/vocab/MISAG_ref_biomaterial) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_ref_db.md b/mixs6/misag_ref_db.md new file mode 100644 index 00000000..d0448aec --- /dev/null +++ b/mixs6/misag_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_ref_db + + + + +URI: [mixs.vocab:MISAG_ref_db](https://w3id.org/mixs/vocab/MISAG_ref_db) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_rel_to_oxygen.md b/mixs6/misag_rel_to_oxygen.md new file mode 100644 index 00000000..63343978 --- /dev/null +++ b/mixs6/misag_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_rel_to_oxygen + + + + +URI: [mixs.vocab:MISAG_rel_to_oxygen](https://w3id.org/mixs/vocab/MISAG_rel_to_oxygen) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_samp_mat_process.md b/mixs6/misag_samp_mat_process.md new file mode 100644 index 00000000..f32b89e8 --- /dev/null +++ b/mixs6/misag_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_samp_mat_process + + + + +URI: [mixs.vocab:MISAG_samp_mat_process](https://w3id.org/mixs/vocab/MISAG_samp_mat_process) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_samp_size.md b/mixs6/misag_samp_size.md new file mode 100644 index 00000000..942a6bc7 --- /dev/null +++ b/mixs6/misag_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_samp_size + + + + +URI: [mixs.vocab:MISAG_samp_size](https://w3id.org/mixs/vocab/MISAG_samp_size) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_sample_name.md b/mixs6/misag_sample_name.md new file mode 100644 index 00000000..15c9fa8d --- /dev/null +++ b/mixs6/misag_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_sample_name + + + + +URI: [mixs.vocab:MISAG_sample_name](https://w3id.org/mixs/vocab/MISAG_sample_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_seq_meth.md b/mixs6/misag_seq_meth.md new file mode 100644 index 00000000..2b28e8e6 --- /dev/null +++ b/mixs6/misag_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_seq_meth + + + + +URI: [mixs.vocab:MISAG_seq_meth](https://w3id.org/mixs/vocab/MISAG_seq_meth) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_sim_search_meth.md b/mixs6/misag_sim_search_meth.md new file mode 100644 index 00000000..0f30eb12 --- /dev/null +++ b/mixs6/misag_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_sim_search_meth + + + + +URI: [mixs.vocab:MISAG_sim_search_meth](https://w3id.org/mixs/vocab/MISAG_sim_search_meth) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_single_cell_lysis_appr.md b/mixs6/misag_single_cell_lysis_appr.md new file mode 100644 index 00000000..ad7a24d0 --- /dev/null +++ b/mixs6/misag_single_cell_lysis_appr.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_single_cell_lysis_appr + + + + +URI: [mixs.vocab:MISAG_single_cell_lysis_appr](https://w3id.org/mixs/vocab/MISAG_single_cell_lysis_appr) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [single_cell_lysis_appr](single_cell_lysis_appr.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_single_cell_lysis_prot.md b/mixs6/misag_single_cell_lysis_prot.md new file mode 100644 index 00000000..da94e88a --- /dev/null +++ b/mixs6/misag_single_cell_lysis_prot.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_single_cell_lysis_prot + + + + +URI: [mixs.vocab:MISAG_single_cell_lysis_prot](https://w3id.org/mixs/vocab/MISAG_single_cell_lysis_prot) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [single_cell_lysis_prot](single_cell_lysis_prot.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_size_frac.md b/mixs6/misag_size_frac.md new file mode 100644 index 00000000..a1faa0c5 --- /dev/null +++ b/mixs6/misag_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_size_frac + + + + +URI: [mixs.vocab:MISAG_size_frac](https://w3id.org/mixs/vocab/MISAG_size_frac) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_sop.md b/mixs6/misag_sop.md new file mode 100644 index 00000000..efdc3ebc --- /dev/null +++ b/mixs6/misag_sop.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_sop + + + + +URI: [mixs.vocab:MISAG_sop](https://w3id.org/mixs/vocab/MISAG_sop) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_sort_tech.md b/mixs6/misag_sort_tech.md new file mode 100644 index 00000000..96540572 --- /dev/null +++ b/mixs6/misag_sort_tech.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_sort_tech + + + + +URI: [mixs.vocab:MISAG_sort_tech](https://w3id.org/mixs/vocab/MISAG_sort_tech) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [sort_tech](sort_tech.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_source_mat_id.md b/mixs6/misag_source_mat_id.md new file mode 100644 index 00000000..4c673c81 --- /dev/null +++ b/mixs6/misag_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_source_mat_id + + + + +URI: [mixs.vocab:MISAG_source_mat_id](https://w3id.org/mixs/vocab/MISAG_source_mat_id) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_submitted_to_insdc.md b/mixs6/misag_submitted_to_insdc.md new file mode 100644 index 00000000..31906e60 --- /dev/null +++ b/mixs6/misag_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_submitted_to_insdc + + + + +URI: [mixs.vocab:MISAG_submitted_to_insdc](https://w3id.org/mixs/vocab/MISAG_submitted_to_insdc) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_tax_class.md b/mixs6/misag_tax_class.md new file mode 100644 index 00000000..edc6dff0 --- /dev/null +++ b/mixs6/misag_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_tax_class + + + + +URI: [mixs.vocab:MISAG_tax_class](https://w3id.org/mixs/vocab/MISAG_tax_class) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_tax_ident.md b/mixs6/misag_tax_ident.md new file mode 100644 index 00000000..55fa12df --- /dev/null +++ b/mixs6/misag_tax_ident.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_tax_ident + + + + +URI: [mixs.vocab:MISAG_tax_ident](https://w3id.org/mixs/vocab/MISAG_tax_ident) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_trna_ext_software.md b/mixs6/misag_trna_ext_software.md new file mode 100644 index 00000000..9a0e5cc8 --- /dev/null +++ b/mixs6/misag_trna_ext_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_trna_ext_software + + + + +URI: [mixs.vocab:MISAG_trna_ext_software](https://w3id.org/mixs/vocab/MISAG_trna_ext_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trna_ext_software](trna_ext_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_trnas.md b/mixs6/misag_trnas.md new file mode 100644 index 00000000..13c4ca45 --- /dev/null +++ b/mixs6/misag_trnas.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_trnas + + + + +URI: [mixs.vocab:MISAG_trnas](https://w3id.org/mixs/vocab/MISAG_trnas) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trnas](trnas.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_url.md b/mixs6/misag_url.md new file mode 100644 index 00000000..f032f1fb --- /dev/null +++ b/mixs6/misag_url.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_url + + + + +URI: [mixs.vocab:MISAG_url](https://w3id.org/mixs/vocab/MISAG_url) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_wga_amp_appr.md b/mixs6/misag_wga_amp_appr.md new file mode 100644 index 00000000..053f81e9 --- /dev/null +++ b/mixs6/misag_wga_amp_appr.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_wga_amp_appr + + + + +URI: [mixs.vocab:MISAG_wga_amp_appr](https://w3id.org/mixs/vocab/MISAG_wga_amp_appr) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [wga_amp_appr](wga_amp_appr.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_wga_amp_kit.md b/mixs6/misag_wga_amp_kit.md new file mode 100644 index 00000000..7e76763c --- /dev/null +++ b/mixs6/misag_wga_amp_kit.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_wga_amp_kit + + + + +URI: [mixs.vocab:MISAG_wga_amp_kit](https://w3id.org/mixs/vocab/MISAG_wga_amp_kit) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [wga_amp_kit](wga_amp_kit.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_x_16s_recover.md b/mixs6/misag_x_16s_recover.md new file mode 100644 index 00000000..d867584d --- /dev/null +++ b/mixs6/misag_x_16s_recover.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_x_16s_recover + + + + +URI: [mixs.vocab:MISAG_x_16s_recover](https://w3id.org/mixs/vocab/MISAG_x_16s_recover) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [x_16s_recover](x_16s_recover.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misc_param.md b/mixs6/misc_param.md new file mode 100644 index 00000000..b1fff5ea --- /dev/null +++ b/mixs6/misc_param.md @@ -0,0 +1,227 @@ + +# Slot: misc_param + + +Any other measurement performed or parameter collected, that is not listed here + +URI: [mixs.vocab:misc_param](https://w3id.org/mixs/vocab/misc_param) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | miscellaneous parameter | +| **Mappings:** | | MIXS:0000752 | +| **Comments:** | | Expected value: parameter name;measurement value | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 16 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='Bicarbonate ion concentration;2075 micromole per kilogram', description=None) | + diff --git a/mixs6/miuvig_adapters.md b/mixs6/miuvig_adapters.md new file mode 100644 index 00000000..e15f4bb3 --- /dev/null +++ b/mixs6/miuvig_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_adapters + + + + +URI: [mixs.vocab:MIUVIG_adapters](https://w3id.org/mixs/vocab/MIUVIG_adapters) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_annot.md b/mixs6/miuvig_annot.md new file mode 100644 index 00000000..5eeab41a --- /dev/null +++ b/mixs6/miuvig_annot.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_annot + + + + +URI: [mixs.vocab:MIUVIG_annot](https://w3id.org/mixs/vocab/MIUVIG_annot) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_assembly_name.md b/mixs6/miuvig_assembly_name.md new file mode 100644 index 00000000..7d398981 --- /dev/null +++ b/mixs6/miuvig_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_assembly_name + + + + +URI: [mixs.vocab:MIUVIG_assembly_name](https://w3id.org/mixs/vocab/MIUVIG_assembly_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_assembly_qual.md b/mixs6/miuvig_assembly_qual.md new file mode 100644 index 00000000..515a782f --- /dev/null +++ b/mixs6/miuvig_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_assembly_qual + + + + +URI: [mixs.vocab:MIUVIG_assembly_qual](https://w3id.org/mixs/vocab/MIUVIG_assembly_qual) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_assembly_software.md b/mixs6/miuvig_assembly_software.md new file mode 100644 index 00000000..91e41a50 --- /dev/null +++ b/mixs6/miuvig_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_assembly_software + + + + +URI: [mixs.vocab:MIUVIG_assembly_software](https://w3id.org/mixs/vocab/MIUVIG_assembly_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_bin_param.md b/mixs6/miuvig_bin_param.md new file mode 100644 index 00000000..9e9cad62 --- /dev/null +++ b/mixs6/miuvig_bin_param.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_bin_param + + + + +URI: [mixs.vocab:MIUVIG_bin_param](https://w3id.org/mixs/vocab/MIUVIG_bin_param) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [bin_param](bin_param.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_bin_software.md b/mixs6/miuvig_bin_software.md new file mode 100644 index 00000000..3acea16e --- /dev/null +++ b/mixs6/miuvig_bin_software.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_bin_software + + + + +URI: [mixs.vocab:MIUVIG_bin_software](https://w3id.org/mixs/vocab/MIUVIG_bin_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [bin_software](bin_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_biotic_relationship.md b/mixs6/miuvig_biotic_relationship.md new file mode 100644 index 00000000..ba1d68ed --- /dev/null +++ b/mixs6/miuvig_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_biotic_relationship + + + + +URI: [mixs.vocab:MIUVIG_biotic_relationship](https://w3id.org/mixs/vocab/MIUVIG_biotic_relationship) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_collection_date.md b/mixs6/miuvig_collection_date.md new file mode 100644 index 00000000..8558aa5c --- /dev/null +++ b/mixs6/miuvig_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_collection_date + + + + +URI: [mixs.vocab:MIUVIG_collection_date](https://w3id.org/mixs/vocab/MIUVIG_collection_date) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [Date](types/Date.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_compl_appr.md b/mixs6/miuvig_compl_appr.md new file mode 100644 index 00000000..165316b6 --- /dev/null +++ b/mixs6/miuvig_compl_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_compl_appr + + + + +URI: [mixs.vocab:MIUVIG_compl_appr](https://w3id.org/mixs/vocab/MIUVIG_compl_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [compl_appr](compl_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_compl_score.md b/mixs6/miuvig_compl_score.md new file mode 100644 index 00000000..ed398660 --- /dev/null +++ b/mixs6/miuvig_compl_score.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_compl_score + + + + +URI: [mixs.vocab:MIUVIG_compl_score](https://w3id.org/mixs/vocab/MIUVIG_compl_score) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_compl_software.md b/mixs6/miuvig_compl_software.md new file mode 100644 index 00000000..c5273c3b --- /dev/null +++ b/mixs6/miuvig_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_compl_software + + + + +URI: [mixs.vocab:MIUVIG_compl_software](https://w3id.org/mixs/vocab/MIUVIG_compl_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_detec_type.md b/mixs6/miuvig_detec_type.md new file mode 100644 index 00000000..7098fffd --- /dev/null +++ b/mixs6/miuvig_detec_type.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_detec_type + + + + +URI: [mixs.vocab:MIUVIG_detec_type](https://w3id.org/mixs/vocab/MIUVIG_detec_type) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [detec_type](detec_type.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_env_broad_scale.md b/mixs6/miuvig_env_broad_scale.md new file mode 100644 index 00000000..0db123de --- /dev/null +++ b/mixs6/miuvig_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_env_broad_scale + + + + +URI: [mixs.vocab:MIUVIG_env_broad_scale](https://w3id.org/mixs/vocab/MIUVIG_env_broad_scale) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_env_local_scale.md b/mixs6/miuvig_env_local_scale.md new file mode 100644 index 00000000..f27eac13 --- /dev/null +++ b/mixs6/miuvig_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_env_local_scale + + + + +URI: [mixs.vocab:MIUVIG_env_local_scale](https://w3id.org/mixs/vocab/MIUVIG_env_local_scale) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_env_medium.md b/mixs6/miuvig_env_medium.md new file mode 100644 index 00000000..b58ac09a --- /dev/null +++ b/mixs6/miuvig_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_env_medium + + + + +URI: [mixs.vocab:MIUVIG_env_medium](https://w3id.org/mixs/vocab/MIUVIG_env_medium) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_env_package.md b/mixs6/miuvig_env_package.md new file mode 100644 index 00000000..ab3fcefc --- /dev/null +++ b/mixs6/miuvig_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_env_package + + + + +URI: [mixs.vocab:MIUVIG_env_package](https://w3id.org/mixs/vocab/MIUVIG_env_package) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_estimated_size.md b/mixs6/miuvig_estimated_size.md new file mode 100644 index 00000000..f1d7ffd3 --- /dev/null +++ b/mixs6/miuvig_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_estimated_size + + + + +URI: [mixs.vocab:MIUVIG_estimated_size](https://w3id.org/mixs/vocab/MIUVIG_estimated_size) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_experimental_factor.md b/mixs6/miuvig_experimental_factor.md new file mode 100644 index 00000000..6d32d32e --- /dev/null +++ b/mixs6/miuvig_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_experimental_factor + + + + +URI: [mixs.vocab:MIUVIG_experimental_factor](https://w3id.org/mixs/vocab/MIUVIG_experimental_factor) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_feat_pred.md b/mixs6/miuvig_feat_pred.md new file mode 100644 index 00000000..74b50c64 --- /dev/null +++ b/mixs6/miuvig_feat_pred.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_feat_pred + + + + +URI: [mixs.vocab:MIUVIG_feat_pred](https://w3id.org/mixs/vocab/MIUVIG_feat_pred) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_geo_loc_name.md b/mixs6/miuvig_geo_loc_name.md new file mode 100644 index 00000000..db0ca0f9 --- /dev/null +++ b/mixs6/miuvig_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_geo_loc_name + + + + +URI: [mixs.vocab:MIUVIG_geo_loc_name](https://w3id.org/mixs/vocab/MIUVIG_geo_loc_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_host_pred_appr.md b/mixs6/miuvig_host_pred_appr.md new file mode 100644 index 00000000..51f76cc6 --- /dev/null +++ b/mixs6/miuvig_host_pred_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_host_pred_appr + + + + +URI: [mixs.vocab:MIUVIG_host_pred_appr](https://w3id.org/mixs/vocab/MIUVIG_host_pred_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [host_pred_appr](host_pred_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_host_pred_est_acc.md b/mixs6/miuvig_host_pred_est_acc.md new file mode 100644 index 00000000..0d66a240 --- /dev/null +++ b/mixs6/miuvig_host_pred_est_acc.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_host_pred_est_acc + + + + +URI: [mixs.vocab:MIUVIG_host_pred_est_acc](https://w3id.org/mixs/vocab/MIUVIG_host_pred_est_acc) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_pred_est_acc](host_pred_est_acc.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_host_spec_range.md b/mixs6/miuvig_host_spec_range.md new file mode 100644 index 00000000..16c57982 --- /dev/null +++ b/mixs6/miuvig_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_host_spec_range + + + + +URI: [mixs.vocab:MIUVIG_host_spec_range](https://w3id.org/mixs/vocab/MIUVIG_host_spec_range) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_investigation_type.md b/mixs6/miuvig_investigation_type.md new file mode 100644 index 00000000..47fab6bc --- /dev/null +++ b/mixs6/miuvig_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_investigation_type + + + + +URI: [mixs.vocab:MIUVIG_investigation_type](https://w3id.org/mixs/vocab/MIUVIG_investigation_type) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_lat_lon.md b/mixs6/miuvig_lat_lon.md new file mode 100644 index 00000000..5e10ade0 --- /dev/null +++ b/mixs6/miuvig_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_lat_lon + + + + +URI: [mixs.vocab:MIUVIG_lat_lon](https://w3id.org/mixs/vocab/MIUVIG_lat_lon) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_lib_layout.md b/mixs6/miuvig_lib_layout.md new file mode 100644 index 00000000..c586c195 --- /dev/null +++ b/mixs6/miuvig_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_layout + + + + +URI: [mixs.vocab:MIUVIG_lib_layout](https://w3id.org/mixs/vocab/MIUVIG_lib_layout) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_reads_seqd.md b/mixs6/miuvig_lib_reads_seqd.md new file mode 100644 index 00000000..dd73845c --- /dev/null +++ b/mixs6/miuvig_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_reads_seqd + + + + +URI: [mixs.vocab:MIUVIG_lib_reads_seqd](https://w3id.org/mixs/vocab/MIUVIG_lib_reads_seqd) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_screen.md b/mixs6/miuvig_lib_screen.md new file mode 100644 index 00000000..b165ba37 --- /dev/null +++ b/mixs6/miuvig_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_screen + + + + +URI: [mixs.vocab:MIUVIG_lib_screen](https://w3id.org/mixs/vocab/MIUVIG_lib_screen) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_size.md b/mixs6/miuvig_lib_size.md new file mode 100644 index 00000000..d90a7681 --- /dev/null +++ b/mixs6/miuvig_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_size + + + + +URI: [mixs.vocab:MIUVIG_lib_size](https://w3id.org/mixs/vocab/MIUVIG_lib_size) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_vector.md b/mixs6/miuvig_lib_vector.md new file mode 100644 index 00000000..784f3acc --- /dev/null +++ b/mixs6/miuvig_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_vector + + + + +URI: [mixs.vocab:MIUVIG_lib_vector](https://w3id.org/mixs/vocab/MIUVIG_lib_vector) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_mag_cov_software.md b/mixs6/miuvig_mag_cov_software.md new file mode 100644 index 00000000..a3014ec6 --- /dev/null +++ b/mixs6/miuvig_mag_cov_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_mag_cov_software + + + + +URI: [mixs.vocab:MIUVIG_mag_cov_software](https://w3id.org/mixs/vocab/MIUVIG_mag_cov_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [mag_cov_software](mag_cov_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_mid.md b/mixs6/miuvig_mid.md new file mode 100644 index 00000000..7706eee3 --- /dev/null +++ b/mixs6/miuvig_mid.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_mid + + + + +URI: [mixs.vocab:MIUVIG_mid](https://w3id.org/mixs/vocab/MIUVIG_mid) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_nucl_acid_amp.md b/mixs6/miuvig_nucl_acid_amp.md new file mode 100644 index 00000000..c1a844bd --- /dev/null +++ b/mixs6/miuvig_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_nucl_acid_amp + + + + +URI: [mixs.vocab:MIUVIG_nucl_acid_amp](https://w3id.org/mixs/vocab/MIUVIG_nucl_acid_amp) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_nucl_acid_ext.md b/mixs6/miuvig_nucl_acid_ext.md new file mode 100644 index 00000000..8ac66447 --- /dev/null +++ b/mixs6/miuvig_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_nucl_acid_ext + + + + +URI: [mixs.vocab:MIUVIG_nucl_acid_ext](https://w3id.org/mixs/vocab/MIUVIG_nucl_acid_ext) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_number_contig.md b/mixs6/miuvig_number_contig.md new file mode 100644 index 00000000..65153efb --- /dev/null +++ b/mixs6/miuvig_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_number_contig + + + + +URI: [mixs.vocab:MIUVIG_number_contig](https://w3id.org/mixs/vocab/MIUVIG_number_contig) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_pathogenicity.md b/mixs6/miuvig_pathogenicity.md new file mode 100644 index 00000000..a8513c3d --- /dev/null +++ b/mixs6/miuvig_pathogenicity.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_pathogenicity + + + + +URI: [mixs.vocab:MIUVIG_pathogenicity](https://w3id.org/mixs/vocab/MIUVIG_pathogenicity) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_pred_genome_struc.md b/mixs6/miuvig_pred_genome_struc.md new file mode 100644 index 00000000..e65cacfe --- /dev/null +++ b/mixs6/miuvig_pred_genome_struc.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_pred_genome_struc + + + + +URI: [mixs.vocab:MIUVIG_pred_genome_struc](https://w3id.org/mixs/vocab/MIUVIG_pred_genome_struc) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [pred_genome_struc](pred_genome_struc.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_pred_genome_type.md b/mixs6/miuvig_pred_genome_type.md new file mode 100644 index 00000000..92bb1df7 --- /dev/null +++ b/mixs6/miuvig_pred_genome_type.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_pred_genome_type + + + + +URI: [mixs.vocab:MIUVIG_pred_genome_type](https://w3id.org/mixs/vocab/MIUVIG_pred_genome_type) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [pred_genome_type](pred_genome_type.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_project_name.md b/mixs6/miuvig_project_name.md new file mode 100644 index 00000000..fdde3b1e --- /dev/null +++ b/mixs6/miuvig_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_project_name + + + + +URI: [mixs.vocab:MIUVIG_project_name](https://w3id.org/mixs/vocab/MIUVIG_project_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_reassembly_bin.md b/mixs6/miuvig_reassembly_bin.md new file mode 100644 index 00000000..b22bac5c --- /dev/null +++ b/mixs6/miuvig_reassembly_bin.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_reassembly_bin + + + + +URI: [mixs.vocab:MIUVIG_reassembly_bin](https://w3id.org/mixs/vocab/MIUVIG_reassembly_bin) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [reassembly_bin](reassembly_bin.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_ref_biomaterial.md b/mixs6/miuvig_ref_biomaterial.md new file mode 100644 index 00000000..a31d3e4d --- /dev/null +++ b/mixs6/miuvig_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_ref_biomaterial + + + + +URI: [mixs.vocab:MIUVIG_ref_biomaterial](https://w3id.org/mixs/vocab/MIUVIG_ref_biomaterial) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_ref_db.md b/mixs6/miuvig_ref_db.md new file mode 100644 index 00000000..45160b73 --- /dev/null +++ b/mixs6/miuvig_ref_db.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_ref_db + + + + +URI: [mixs.vocab:MIUVIG_ref_db](https://w3id.org/mixs/vocab/MIUVIG_ref_db) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_samp_mat_process.md b/mixs6/miuvig_samp_mat_process.md new file mode 100644 index 00000000..60f5db1b --- /dev/null +++ b/mixs6/miuvig_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_samp_mat_process + + + + +URI: [mixs.vocab:MIUVIG_samp_mat_process](https://w3id.org/mixs/vocab/MIUVIG_samp_mat_process) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_samp_size.md b/mixs6/miuvig_samp_size.md new file mode 100644 index 00000000..eca8e8fa --- /dev/null +++ b/mixs6/miuvig_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_samp_size + + + + +URI: [mixs.vocab:MIUVIG_samp_size](https://w3id.org/mixs/vocab/MIUVIG_samp_size) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_sample_name.md b/mixs6/miuvig_sample_name.md new file mode 100644 index 00000000..03935225 --- /dev/null +++ b/mixs6/miuvig_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_sample_name + + + + +URI: [mixs.vocab:MIUVIG_sample_name](https://w3id.org/mixs/vocab/MIUVIG_sample_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_seq_meth.md b/mixs6/miuvig_seq_meth.md new file mode 100644 index 00000000..00687d2f --- /dev/null +++ b/mixs6/miuvig_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_seq_meth + + + + +URI: [mixs.vocab:MIUVIG_seq_meth](https://w3id.org/mixs/vocab/MIUVIG_seq_meth) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_sim_search_meth.md b/mixs6/miuvig_sim_search_meth.md new file mode 100644 index 00000000..67926fe9 --- /dev/null +++ b/mixs6/miuvig_sim_search_meth.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sim_search_meth + + + + +URI: [mixs.vocab:MIUVIG_sim_search_meth](https://w3id.org/mixs/vocab/MIUVIG_sim_search_meth) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_single_cell_lysis_appr.md b/mixs6/miuvig_single_cell_lysis_appr.md new file mode 100644 index 00000000..da873597 --- /dev/null +++ b/mixs6/miuvig_single_cell_lysis_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_single_cell_lysis_appr + + + + +URI: [mixs.vocab:MIUVIG_single_cell_lysis_appr](https://w3id.org/mixs/vocab/MIUVIG_single_cell_lysis_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [single_cell_lysis_appr](single_cell_lysis_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_single_cell_lysis_prot.md b/mixs6/miuvig_single_cell_lysis_prot.md new file mode 100644 index 00000000..2445d9aa --- /dev/null +++ b/mixs6/miuvig_single_cell_lysis_prot.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_single_cell_lysis_prot + + + + +URI: [mixs.vocab:MIUVIG_single_cell_lysis_prot](https://w3id.org/mixs/vocab/MIUVIG_single_cell_lysis_prot) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [single_cell_lysis_prot](single_cell_lysis_prot.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_size_frac.md b/mixs6/miuvig_size_frac.md new file mode 100644 index 00000000..509e9bc0 --- /dev/null +++ b/mixs6/miuvig_size_frac.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_size_frac + + + + +URI: [mixs.vocab:MIUVIG_size_frac](https://w3id.org/mixs/vocab/MIUVIG_size_frac) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_sop.md b/mixs6/miuvig_sop.md new file mode 100644 index 00000000..3289ec69 --- /dev/null +++ b/mixs6/miuvig_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sop + + + + +URI: [mixs.vocab:MIUVIG_sop](https://w3id.org/mixs/vocab/MIUVIG_sop) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_sort_tech.md b/mixs6/miuvig_sort_tech.md new file mode 100644 index 00000000..6d6a6e28 --- /dev/null +++ b/mixs6/miuvig_sort_tech.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sort_tech + + + + +URI: [mixs.vocab:MIUVIG_sort_tech](https://w3id.org/mixs/vocab/MIUVIG_sort_tech) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [sort_tech](sort_tech.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_source_mat_id.md b/mixs6/miuvig_source_mat_id.md new file mode 100644 index 00000000..5be280f7 --- /dev/null +++ b/mixs6/miuvig_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_source_mat_id + + + + +URI: [mixs.vocab:MIUVIG_source_mat_id](https://w3id.org/mixs/vocab/MIUVIG_source_mat_id) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_source_uvig.md b/mixs6/miuvig_source_uvig.md new file mode 100644 index 00000000..8f4e0d1c --- /dev/null +++ b/mixs6/miuvig_source_uvig.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_source_uvig + + + + +URI: [mixs.vocab:MIUVIG_source_uvig](https://w3id.org/mixs/vocab/MIUVIG_source_uvig) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [source_uvig](source_uvig.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_specific_host.md b/mixs6/miuvig_specific_host.md new file mode 100644 index 00000000..554e8924 --- /dev/null +++ b/mixs6/miuvig_specific_host.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_specific_host + + + + +URI: [mixs.vocab:MIUVIG_specific_host](https://w3id.org/mixs/vocab/MIUVIG_specific_host) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_submitted_to_insdc.md b/mixs6/miuvig_submitted_to_insdc.md new file mode 100644 index 00000000..235fc6a0 --- /dev/null +++ b/mixs6/miuvig_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_submitted_to_insdc + + + + +URI: [mixs.vocab:MIUVIG_submitted_to_insdc](https://w3id.org/mixs/vocab/MIUVIG_submitted_to_insdc) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_tax_class.md b/mixs6/miuvig_tax_class.md new file mode 100644 index 00000000..816b70b0 --- /dev/null +++ b/mixs6/miuvig_tax_class.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_tax_class + + + + +URI: [mixs.vocab:MIUVIG_tax_class](https://w3id.org/mixs/vocab/MIUVIG_tax_class) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_tax_ident.md b/mixs6/miuvig_tax_ident.md new file mode 100644 index 00000000..14c3f884 --- /dev/null +++ b/mixs6/miuvig_tax_ident.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_tax_ident + + + + +URI: [mixs.vocab:MIUVIG_tax_ident](https://w3id.org/mixs/vocab/MIUVIG_tax_ident) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_trna_ext_software.md b/mixs6/miuvig_trna_ext_software.md new file mode 100644 index 00000000..95f2b597 --- /dev/null +++ b/mixs6/miuvig_trna_ext_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_trna_ext_software + + + + +URI: [mixs.vocab:MIUVIG_trna_ext_software](https://w3id.org/mixs/vocab/MIUVIG_trna_ext_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trna_ext_software](trna_ext_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_trnas.md b/mixs6/miuvig_trnas.md new file mode 100644 index 00000000..4ec928f5 --- /dev/null +++ b/mixs6/miuvig_trnas.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_trnas + + + + +URI: [mixs.vocab:MIUVIG_trnas](https://w3id.org/mixs/vocab/MIUVIG_trnas) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trnas](trnas.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_url.md b/mixs6/miuvig_url.md new file mode 100644 index 00000000..9219ddb4 --- /dev/null +++ b/mixs6/miuvig_url.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_url + + + + +URI: [mixs.vocab:MIUVIG_url](https://w3id.org/mixs/vocab/MIUVIG_url) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_vir_ident_software.md b/mixs6/miuvig_vir_ident_software.md new file mode 100644 index 00000000..64c4c086 --- /dev/null +++ b/mixs6/miuvig_vir_ident_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_vir_ident_software + + + + +URI: [mixs.vocab:MIUVIG_vir_ident_software](https://w3id.org/mixs/vocab/MIUVIG_vir_ident_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [vir_ident_software](vir_ident_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_virus_enrich_appr.md b/mixs6/miuvig_virus_enrich_appr.md new file mode 100644 index 00000000..4d9e6441 --- /dev/null +++ b/mixs6/miuvig_virus_enrich_appr.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_virus_enrich_appr + + + + +URI: [mixs.vocab:MIUVIG_virus_enrich_appr](https://w3id.org/mixs/vocab/MIUVIG_virus_enrich_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [virus_enrich_appr](virus_enrich_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_votu_class_appr.md b/mixs6/miuvig_votu_class_appr.md new file mode 100644 index 00000000..b68330ad --- /dev/null +++ b/mixs6/miuvig_votu_class_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_votu_class_appr + + + + +URI: [mixs.vocab:MIUVIG_votu_class_appr](https://w3id.org/mixs/vocab/MIUVIG_votu_class_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [votu_class_appr](votu_class_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_votu_db.md b/mixs6/miuvig_votu_db.md new file mode 100644 index 00000000..5c4c96c1 --- /dev/null +++ b/mixs6/miuvig_votu_db.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_votu_db + + + + +URI: [mixs.vocab:MIUVIG_votu_db](https://w3id.org/mixs/vocab/MIUVIG_votu_db) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [votu_db](votu_db.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_votu_seq_comp_appr.md b/mixs6/miuvig_votu_seq_comp_appr.md new file mode 100644 index 00000000..71f7abde --- /dev/null +++ b/mixs6/miuvig_votu_seq_comp_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_votu_seq_comp_appr + + + + +URI: [mixs.vocab:MIUVIG_votu_seq_comp_appr](https://w3id.org/mixs/vocab/MIUVIG_votu_seq_comp_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [votu_seq_comp_appr](votu_seq_comp_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_wga_amp_appr.md b/mixs6/miuvig_wga_amp_appr.md new file mode 100644 index 00000000..1710900f --- /dev/null +++ b/mixs6/miuvig_wga_amp_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_wga_amp_appr + + + + +URI: [mixs.vocab:MIUVIG_wga_amp_appr](https://w3id.org/mixs/vocab/MIUVIG_wga_amp_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [wga_amp_appr](wga_amp_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_wga_amp_kit.md b/mixs6/miuvig_wga_amp_kit.md new file mode 100644 index 00000000..b19690ac --- /dev/null +++ b/mixs6/miuvig_wga_amp_kit.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_wga_amp_kit + + + + +URI: [mixs.vocab:MIUVIG_wga_amp_kit](https://w3id.org/mixs/vocab/MIUVIG_wga_amp_kit) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [wga_amp_kit](wga_amp_kit.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mixs_extension_field.md b/mixs6/mixs_extension_field.md new file mode 100644 index 00000000..d64e407f --- /dev/null +++ b/mixs6/mixs_extension_field.md @@ -0,0 +1,22 @@ + +# Slot: mixs_extension_field + + + + +URI: [mixs.vocab:mixs_extension_field](https://w3id.org/mixs/vocab/mixs_extension_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [env_package](env_package.md) + +## Used by + diff --git a/mixs6/n_alkanes.md b/mixs6/n_alkanes.md new file mode 100644 index 00000000..d5b83e79 --- /dev/null +++ b/mixs6/n_alkanes.md @@ -0,0 +1,72 @@ + +# Slot: n_alkanes + + +Concentration of n-alkanes; can include multiple n-alkanes + +URI: [mixs.vocab:n_alkanes](https://w3id.org/mixs/vocab/n_alkanes) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | n-alkanes | +| **Mappings:** | | MIXS:0000503 | +| **Comments:** | | Expected value: n-alkane name;measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='n-hexadecane;100 milligram per liter', description=None) | + diff --git a/mixs6/nitrate.md b/mixs6/nitrate.md new file mode 100644 index 00000000..c9687ad8 --- /dev/null +++ b/mixs6/nitrate.md @@ -0,0 +1,120 @@ + +# Slot: nitrate + + +Concentration of nitrate in the sample + +URI: [mixs.vocab:nitrate](https://w3id.org/mixs/vocab/nitrate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nitrate | +| **Mappings:** | | MIXS:0000425 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 61.0 | +| | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='65 micromole per liter', description=None) | + diff --git a/mixs6/nitrite.md b/mixs6/nitrite.md new file mode 100644 index 00000000..1b4b40a9 --- /dev/null +++ b/mixs6/nitrite.md @@ -0,0 +1,108 @@ + +# Slot: nitrite + + +Concentration of nitrite in the sample + +URI: [mixs.vocab:nitrite](https://w3id.org/mixs/vocab/nitrite) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nitrite | +| **Mappings:** | | MIXS:0000426 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 62.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.5 micromole per liter', description=None) | + diff --git a/mixs6/nitro.md b/mixs6/nitro.md new file mode 100644 index 00000000..6044ee12 --- /dev/null +++ b/mixs6/nitro.md @@ -0,0 +1,84 @@ + +# Slot: nitro + + +Concentration of nitrogen (total) + +URI: [mixs.vocab:nitro](https://w3id.org/mixs/vocab/nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nitrogen | +| **Mappings:** | | MIXS:0000504 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='4.2 micromole per liter', description=None) | + diff --git a/mixs6/non_mineral_nutr_regm.md b/mixs6/non_mineral_nutr_regm.md new file mode 100644 index 00000000..7242f472 --- /dev/null +++ b/mixs6/non_mineral_nutr_regm.md @@ -0,0 +1,48 @@ + +# Slot: non_mineral_nutr_regm + + +Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + +URI: [mixs.vocab:non_mineral_nutr_regm](https://w3id.org/mixs/vocab/non_mineral_nutr_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | non-mineral nutrient regimen | +| **Mappings:** | | MIXS:0000571 | +| **Comments:** | | Expected value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/nose_mouth_teeth_throat_disord.md b/mixs6/nose_mouth_teeth_throat_disord.md new file mode 100644 index 00000000..d4a72fa2 --- /dev/null +++ b/mixs6/nose_mouth_teeth_throat_disord.md @@ -0,0 +1,47 @@ + +# Slot: nose_mouth_teeth_throat_disord + + +History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + +URI: [mixs.vocab:nose_mouth_teeth_throat_disord](https://w3id.org/mixs/vocab/nose_mouth_teeth_throat_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nose/mouth/teeth/throat disorder | +| **Mappings:** | | MIXS:0000283 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: human-oral | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/nose_throat_disord.md b/mixs6/nose_throat_disord.md new file mode 100644 index 00000000..0254863e --- /dev/null +++ b/mixs6/nose_throat_disord.md @@ -0,0 +1,47 @@ + +# Slot: nose_throat_disord + + +History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + +URI: [mixs.vocab:nose_throat_disord](https://w3id.org/mixs/vocab/nose_throat_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | lung/nose-throat disorder | +| **Mappings:** | | MIXS:0000270 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 31.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/nucl_acid_amp.md b/mixs6/nucl_acid_amp.md new file mode 100644 index 00000000..4d3c9b1d --- /dev/null +++ b/mixs6/nucl_acid_amp.md @@ -0,0 +1,44 @@ + +# Slot: nucl_acid_amp + + +A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + +URI: [mixs.vocab:nucl_acid_amp](https://w3id.org/mixs/vocab/nucl_acid_amp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nucleic acid amplification | +| **Comments:** | | Expected value: PMID, DOI or URL | +| | | Position: 38.0 | +| **Examples:** | | Example(value='https://phylogenomics.me/protocols/16s-pcr-protocol/', description=None) | + diff --git a/mixs6/nucl_acid_ext.md b/mixs6/nucl_acid_ext.md new file mode 100644 index 00000000..7bb2add5 --- /dev/null +++ b/mixs6/nucl_acid_ext.md @@ -0,0 +1,44 @@ + +# Slot: nucl_acid_ext + + +A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + +URI: [mixs.vocab:nucl_acid_ext](https://w3id.org/mixs/vocab/nucl_acid_ext) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nucleic acid extraction | +| **Comments:** | | Expected value: PMID, DOI or URL | +| | | Position: 37.0 | +| **Examples:** | | Example(value='https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf', description=None) | + diff --git a/mixs6/nucleic_acid_sequence_source_field.md b/mixs6/nucleic_acid_sequence_source_field.md new file mode 100644 index 00000000..733b61ed --- /dev/null +++ b/mixs6/nucleic_acid_sequence_source_field.md @@ -0,0 +1,45 @@ + +# Slot: nucleic_acid_sequence_source_field + + + + +URI: [mixs.vocab:nucleic_acid_sequence_source_field](https://w3id.org/mixs/vocab/nucleic_acid_sequence_source_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [biotic_relationship](biotic_relationship.md) + * [encoded_traits](encoded_traits.md) + * [estimated_size](estimated_size.md) + * [extrachrom_elements](extrachrom_elements.md) + * [health_disease_stat](health_disease_stat.md) + * [host_spec_range](host_spec_range.md) + * [isol_growth_condt](isol_growth_condt.md) + * [num_replicons](num_replicons.md) + * [pathogenicity](pathogenicity.md) + * [ploidy](ploidy.md) + * [propagation](propagation.md) + * [ref_biomaterial](ref_biomaterial.md) + * [rel_to_oxygen](rel_to_oxygen.md) + * [samp_mat_process](samp_mat_process.md) + * [samp_size](samp_size.md) + * [sample_collect_device](sample_collect_device.md) + * [sample_collect_method](sample_collect_method.md) + * [size_frac](size_frac.md) + * [source_mat_id](source_mat_id.md) + * [source_uvig](source_uvig.md) + * [specific_host](specific_host.md) + * [subspecf_gen_lin](subspecf_gen_lin.md) + * [trophic_level](trophic_level.md) + * [virus_enrich_appr](virus_enrich_appr.md) + +## Used by + diff --git a/mixs6/num_replicons.md b/mixs6/num_replicons.md new file mode 100644 index 00000000..fe07231a --- /dev/null +++ b/mixs6/num_replicons.md @@ -0,0 +1,36 @@ + +# Slot: num_replicons + + +Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + +URI: [mixs.vocab:num_replicons](https://w3id.org/mixs/vocab/num_replicons) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of replicons | +| **Comments:** | | Expected value: for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments | +| | | Position: 16.0 | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/number_contig.md b/mixs6/number_contig.md new file mode 100644 index 00000000..e68c4a77 --- /dev/null +++ b/mixs6/number_contig.md @@ -0,0 +1,42 @@ + +# Slot: number_contig + + +Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + +URI: [mixs.vocab:number_contig](https://w3id.org/mixs/vocab/number_contig) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞number_contig](ME_number_contig.md) + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) + * [MIGS org➞number_contig](MIGS_org_number_contig.md) + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) + * [MIMAG➞number_contig](MIMAG_number_contig.md) + * [MISAG➞number_contig](MISAG_number_contig.md) + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of contigs | +| **Comments:** | | Expected value: value | +| | | Position: 58.0 | +| **Examples:** | | Example(value='40', description=None) | + diff --git a/mixs6/number_pets.md b/mixs6/number_pets.md new file mode 100644 index 00000000..ca1b800d --- /dev/null +++ b/mixs6/number_pets.md @@ -0,0 +1,47 @@ + +# Slot: number_pets + + +The number of pets residing in the sampled space + +URI: [mixs.vocab:number_pets](https://w3id.org/mixs/vocab/number_pets) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of pets | +| **Mappings:** | | MIXS:0000231 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 93.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/number_plants.md b/mixs6/number_plants.md new file mode 100644 index 00000000..c2ba253f --- /dev/null +++ b/mixs6/number_plants.md @@ -0,0 +1,47 @@ + +# Slot: number_plants + + +The number of plant(s) in the sampling space + +URI: [mixs.vocab:number_plants](https://w3id.org/mixs/vocab/number_plants) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of houseplants | +| **Mappings:** | | MIXS:0000230 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 92.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/number_resident.md b/mixs6/number_resident.md new file mode 100644 index 00000000..c2a93503 --- /dev/null +++ b/mixs6/number_resident.md @@ -0,0 +1,47 @@ + +# Slot: number_resident + + +The number of individuals currently occupying in the sampling location + +URI: [mixs.vocab:number_resident](https://w3id.org/mixs/vocab/number_resident) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of residents | +| **Mappings:** | | MIXS:0000232 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 94.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/occup_density_samp.md b/mixs6/occup_density_samp.md new file mode 100644 index 00000000..7aedac03 --- /dev/null +++ b/mixs6/occup_density_samp.md @@ -0,0 +1,47 @@ + +# Slot: occup_density_samp + + +Average number of occupants at time of sampling per square footage + +URI: [mixs.vocab:occup_density_samp](https://w3id.org/mixs/vocab/occup_density_samp) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | occupant density at sampling | +| **Mappings:** | | MIXS:0000217 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 26.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/occup_document.md b/mixs6/occup_document.md new file mode 100644 index 00000000..f3b7cbc3 --- /dev/null +++ b/mixs6/occup_document.md @@ -0,0 +1,47 @@ + +# Slot: occup_document + + +The type of documentation of occupancy + +URI: [mixs.vocab:occup_document](https://w3id.org/mixs/vocab/occup_document) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | occupancy documentation | +| **Mappings:** | | MIXS:0000816 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 95.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='estimate', description=None) | + diff --git a/mixs6/occup_samp.md b/mixs6/occup_samp.md new file mode 100644 index 00000000..165af97d --- /dev/null +++ b/mixs6/occup_samp.md @@ -0,0 +1,47 @@ + +# Slot: occup_samp + + +Number of occupants present at time of sample within the given space + +URI: [mixs.vocab:occup_samp](https://w3id.org/mixs/vocab/occup_samp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | occupancy at sampling | +| **Mappings:** | | MIXS:0000772 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 25.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='10', description=None) | + diff --git a/mixs6/org_carb.md b/mixs6/org_carb.md new file mode 100644 index 00000000..746ff236 --- /dev/null +++ b/mixs6/org_carb.md @@ -0,0 +1,84 @@ + +# Slot: org_carb + + +Concentration of organic carbon + +URI: [mixs.vocab:org_carb](https://w3id.org/mixs/vocab/org_carb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic carbon | +| **Mappings:** | | MIXS:0000508 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1.5 microgram per liter', description=None) | + diff --git a/mixs6/org_matter.md b/mixs6/org_matter.md new file mode 100644 index 00000000..0211396a --- /dev/null +++ b/mixs6/org_matter.md @@ -0,0 +1,84 @@ + +# Slot: org_matter + + +Concentration of organic matter + +URI: [mixs.vocab:org_matter](https://w3id.org/mixs/vocab/org_matter) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic matter | +| **Mappings:** | | MIXS:0000204 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1.75 milligram per cubic meter', description=None) | + diff --git a/mixs6/org_nitro.md b/mixs6/org_nitro.md new file mode 100644 index 00000000..56f72346 --- /dev/null +++ b/mixs6/org_nitro.md @@ -0,0 +1,84 @@ + +# Slot: org_nitro + + +Concentration of organic nitrogen + +URI: [mixs.vocab:org_nitro](https://w3id.org/mixs/vocab/org_nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic nitrogen | +| **Mappings:** | | MIXS:0000205 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='4 micromole per liter', description=None) | + diff --git a/mixs6/org_particles.md b/mixs6/org_particles.md new file mode 100644 index 00000000..9968feb6 --- /dev/null +++ b/mixs6/org_particles.md @@ -0,0 +1,48 @@ + +# Slot: org_particles + + +Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + +URI: [mixs.vocab:org_particles](https://w3id.org/mixs/vocab/org_particles) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic particles | +| **Mappings:** | | MIXS:0000665 | +| **Comments:** | | Expected value: particle name;measurement value | +| | | Preferred unit: gram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/organism_count.md b/mixs6/organism_count.md new file mode 100644 index 00000000..2bb12d1d --- /dev/null +++ b/mixs6/organism_count.md @@ -0,0 +1,228 @@ + +# Slot: organism_count + + +Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + +URI: [mixs.vocab:organism_count](https://w3id.org/mixs/vocab/organism_count) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organism count | +| **Mappings:** | | MIXS:0000103 | +| **Comments:** | | Expected value: organism name;measurement value;enumeration | +| | | Preferred unit: number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 16 packages: air, built environment, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='total prokaryotes;3.5e7 cells per milliliter;qPCR', description=None) | + diff --git a/mixs6/organism_count_qpcr_info.md b/mixs6/organism_count_qpcr_info.md new file mode 100644 index 00000000..178d8b09 --- /dev/null +++ b/mixs6/organism_count_qpcr_info.md @@ -0,0 +1,60 @@ + +# Slot: organism_count_qpcr_info + + +If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + +URI: [mixs.vocab:organism_count_qpcr_info](https://w3id.org/mixs/vocab/organism_count_qpcr_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organism count qPCR information | +| **Mappings:** | | MIXS:0000099 | +| **Comments:** | | Expected value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles | +| | | Preferred unit: number of cells per gram (or ml or cm^2) | +| | | Occurrence: 1 | +| | | Position: 53.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/owc_tvdss.md b/mixs6/owc_tvdss.md new file mode 100644 index 00000000..6431ba91 --- /dev/null +++ b/mixs6/owc_tvdss.md @@ -0,0 +1,48 @@ + +# Slot: owc_tvdss + + +Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + +URI: [mixs.vocab:owc_tvdss](https://w3id.org/mixs/vocab/owc_tvdss) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | oil water contact depth | +| **Mappings:** | | MIXS:0000405 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 15.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/oxy_stat_samp.md b/mixs6/oxy_stat_samp.md new file mode 100644 index 00000000..5a830385 --- /dev/null +++ b/mixs6/oxy_stat_samp.md @@ -0,0 +1,215 @@ + +# Slot: oxy_stat_samp + + +Oxygenation status of sample + +URI: [mixs.vocab:oxy_stat_samp](https://w3id.org/mixs/vocab/oxy_stat_samp) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | oxygenation status of sample | +| **Mappings:** | | MIXS:0000753 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='aerobic', description=None) | + diff --git a/mixs6/oxygen.md b/mixs6/oxygen.md new file mode 100644 index 00000000..22ec1b7f --- /dev/null +++ b/mixs6/oxygen.md @@ -0,0 +1,48 @@ + +# Slot: oxygen + + +Oxygen (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:oxygen](https://w3id.org/mixs/vocab/oxygen) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | oxygen | +| **Mappings:** | | MIXS:0000104 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='600 parts per million', description=None) | + diff --git a/mixs6/part_org_carb.md b/mixs6/part_org_carb.md new file mode 100644 index 00000000..69051815 --- /dev/null +++ b/mixs6/part_org_carb.md @@ -0,0 +1,72 @@ + +# Slot: part_org_carb + + +Concentration of particulate organic carbon + +URI: [mixs.vocab:part_org_carb](https://w3id.org/mixs/vocab/part_org_carb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | particulate organic carbon | +| **Mappings:** | | MIXS:0000515 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='1.92 micromole per liter', description=None) | + diff --git a/mixs6/part_org_nitro.md b/mixs6/part_org_nitro.md new file mode 100644 index 00000000..8289c1cf --- /dev/null +++ b/mixs6/part_org_nitro.md @@ -0,0 +1,48 @@ + +# Slot: part_org_nitro + + +Concentration of particulate organic nitrogen + +URI: [mixs.vocab:part_org_nitro](https://w3id.org/mixs/vocab/part_org_nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | particulate organic nitrogen | +| **Mappings:** | | MIXS:0000719 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.3 micromole per liter', description=None) | + diff --git a/mixs6/particle_class.md b/mixs6/particle_class.md new file mode 100644 index 00000000..f47332ca --- /dev/null +++ b/mixs6/particle_class.md @@ -0,0 +1,48 @@ + +# Slot: particle_class + + +Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + +URI: [mixs.vocab:particle_class](https://w3id.org/mixs/vocab/particle_class) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | particle classification | +| **Mappings:** | | MIXS:0000206 | +| **Comments:** | | Expected value: particle name;measurement value | +| | | Preferred unit: micrometer | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: sediment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/pathogenicity.md b/mixs6/pathogenicity.md new file mode 100644 index 00000000..5c8cf35d --- /dev/null +++ b/mixs6/pathogenicity.md @@ -0,0 +1,38 @@ + +# Slot: pathogenicity + + +To what is the entity pathogenic + +URI: [mixs.vocab:pathogenicity](https://w3id.org/mixs/vocab/pathogenicity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | known pathogenicity | +| **Comments:** | | Expected value: names of organisms that the entity is pathogenic to | +| | | Position: 21.0 | +| **Examples:** | | Example(value='human, animal, plant, fungi, bacteria', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/65 | + diff --git a/mixs6/pcr_cond.md b/mixs6/pcr_cond.md new file mode 100644 index 00000000..f19ef250 --- /dev/null +++ b/mixs6/pcr_cond.md @@ -0,0 +1,35 @@ + +# Slot: pcr_cond + + +Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + +URI: [mixs.vocab:pcr_cond](https://w3id.org/mixs/vocab/pcr_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pcr conditions | +| **Comments:** | | Expected value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles | +| | | Position: 49.0 | +| **Examples:** | | Example(value='initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35', description=None) | + diff --git a/mixs6/pcr_primers.md b/mixs6/pcr_primers.md new file mode 100644 index 00000000..c6ba6049 --- /dev/null +++ b/mixs6/pcr_primers.md @@ -0,0 +1,35 @@ + +# Slot: pcr_primers + + +PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + +URI: [mixs.vocab:pcr_primers](https://w3id.org/mixs/vocab/pcr_primers) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pcr primers | +| **Comments:** | | Expected value: FWD: forward primer sequence;REV:reverse primer sequence | +| | | Position: 46.0 | +| **Examples:** | | Example(value='FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT', description=None) | + diff --git a/mixs6/permeability.md b/mixs6/permeability.md new file mode 100644 index 00000000..6e2e1d11 --- /dev/null +++ b/mixs6/permeability.md @@ -0,0 +1,48 @@ + +# Slot: permeability + + +Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + +URI: [mixs.vocab:permeability](https://w3id.org/mixs/vocab/permeability) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | permeability | +| **Mappings:** | | MIXS:0000404 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: mD | +| | | Occurrence: 1 | +| | | Position: 10.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/perturbation.md b/mixs6/perturbation.md new file mode 100644 index 00000000..b94f6f07 --- /dev/null +++ b/mixs6/perturbation.md @@ -0,0 +1,191 @@ + +# Slot: perturbation + + +Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + +URI: [mixs.vocab:perturbation](https://w3id.org/mixs/vocab/perturbation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | perturbation | +| **Mappings:** | | MIXS:0000754 | +| **Comments:** | | Expected value: perturbation type name;perturbation interval and duration | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 13 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M', description=None) | + diff --git a/mixs6/pesticide_regm.md b/mixs6/pesticide_regm.md new file mode 100644 index 00000000..df0e89a6 --- /dev/null +++ b/mixs6/pesticide_regm.md @@ -0,0 +1,48 @@ + +# Slot: pesticide_regm + + +Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + +URI: [mixs.vocab:pesticide_regm](https://w3id.org/mixs/vocab/pesticide_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pesticide regimen | +| **Mappings:** | | MIXS:0000573 | +| **Comments:** | | Expected value: pesticide name;pesticide amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/pet_farm_animal.md b/mixs6/pet_farm_animal.md new file mode 100644 index 00000000..71efb9cf --- /dev/null +++ b/mixs6/pet_farm_animal.md @@ -0,0 +1,47 @@ + +# Slot: pet_farm_animal + + +Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + +URI: [mixs.vocab:pet_farm_animal](https://w3id.org/mixs/vocab/pet_farm_animal) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | presence of pets or farm animals | +| **Mappings:** | | MIXS:0000267 | +| **Comments:** | | Expected value: presence status;type of animal or pet | +| | | Occurrence: m | +| | | Position: 25.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes; 5 cats', description=None) | + diff --git a/mixs6/petroleum_hydrocarb.md b/mixs6/petroleum_hydrocarb.md new file mode 100644 index 00000000..1cf4434f --- /dev/null +++ b/mixs6/petroleum_hydrocarb.md @@ -0,0 +1,72 @@ + +# Slot: petroleum_hydrocarb + + +Concentration of petroleum hydrocarbon + +URI: [mixs.vocab:petroleum_hydrocarb](https://w3id.org/mixs/vocab/petroleum_hydrocarb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | petroleum hydrocarbon | +| **Mappings:** | | MIXS:0000516 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.05 micromole per liter', description=None) | + diff --git a/mixs6/ph.md b/mixs6/ph.md new file mode 100644 index 00000000..2127ffc6 --- /dev/null +++ b/mixs6/ph.md @@ -0,0 +1,131 @@ + +# Slot: ph + + +Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + +URI: [mixs.vocab:ph](https://w3id.org/mixs/vocab/ph) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pH | +| **Mappings:** | | MIXS:0001001 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 54.0 | +| | | This field is used in: 8 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='7.2', description=None) | + diff --git a/mixs6/ph_meth.md b/mixs6/ph_meth.md new file mode 100644 index 00000000..f82ad2c2 --- /dev/null +++ b/mixs6/ph_meth.md @@ -0,0 +1,47 @@ + +# Slot: ph_meth + + +Reference or method used in determining ph + +URI: [mixs.vocab:ph_meth](https://w3id.org/mixs/vocab/ph_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pH method | +| **Mappings:** | | MIXS:0001106 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 38.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ph_regm.md b/mixs6/ph_regm.md new file mode 100644 index 00000000..cbc96ba3 --- /dev/null +++ b/mixs6/ph_regm.md @@ -0,0 +1,47 @@ + +# Slot: ph_regm + + +Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + +URI: [mixs.vocab:ph_regm](https://w3id.org/mixs/vocab/ph_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pH regimen | +| **Mappings:** | | MIXS:0001056 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/phaeopigments.md b/mixs6/phaeopigments.md new file mode 100644 index 00000000..e2be2905 --- /dev/null +++ b/mixs6/phaeopigments.md @@ -0,0 +1,72 @@ + +# Slot: phaeopigments + + +Concentration of phaeopigments; can include multiple phaeopigments + +URI: [mixs.vocab:phaeopigments](https://w3id.org/mixs/vocab/phaeopigments) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | phaeopigments | +| **Mappings:** | | MIXS:0000180 | +| **Comments:** | | Expected value: phaeopigment name;measurement value | +| | | Preferred unit: milligram per cubic meter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='2.5 milligram per cubic meter', description=None) | + diff --git a/mixs6/phosphate.md b/mixs6/phosphate.md new file mode 100644 index 00000000..915153b0 --- /dev/null +++ b/mixs6/phosphate.md @@ -0,0 +1,96 @@ + +# Slot: phosphate + + +Concentration of phosphate + +URI: [mixs.vocab:phosphate](https://w3id.org/mixs/vocab/phosphate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | phosphate | +| **Mappings:** | | MIXS:0000505 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 5 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='0.7 micromole per liter', description=None) | + diff --git a/mixs6/phosplipid_fatt_acid.md b/mixs6/phosplipid_fatt_acid.md new file mode 100644 index 00000000..c269d966 --- /dev/null +++ b/mixs6/phosplipid_fatt_acid.md @@ -0,0 +1,84 @@ + +# Slot: phosplipid_fatt_acid + + +Concentration of phospholipid fatty acids; can include multiple values + +URI: [mixs.vocab:phosplipid_fatt_acid](https://w3id.org/mixs/vocab/phosplipid_fatt_acid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | phospholipid fatty acid | +| **Mappings:** | | MIXS:0000181 | +| **Comments:** | | Expected value: phospholipid fatty acid name;measurement value | +| | | Preferred unit: mole per gram, mole per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='2.98 milligram per liter', description=None) | + diff --git a/mixs6/photon_flux.md b/mixs6/photon_flux.md new file mode 100644 index 00000000..62411795 --- /dev/null +++ b/mixs6/photon_flux.md @@ -0,0 +1,48 @@ + +# Slot: photon_flux + + +Measurement of photon flux + +URI: [mixs.vocab:photon_flux](https://w3id.org/mixs/vocab/photon_flux) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | photon flux | +| **Mappings:** | | MIXS:0000725 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: number of photons per second per unit area | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='3.926 micromole photons per second per square meter', description=None) | + diff --git a/mixs6/plant_growth_med.md b/mixs6/plant_growth_med.md new file mode 100644 index 00000000..5f78515a --- /dev/null +++ b/mixs6/plant_growth_med.md @@ -0,0 +1,47 @@ + +# Slot: plant_growth_med + + +Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + +URI: [mixs.vocab:plant_growth_med](https://w3id.org/mixs/vocab/plant_growth_med) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant growth medium | +| **Mappings:** | | MIXS:0001057 | +| **Comments:** | | Expected value: EO or enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='hydroponic plant culture media [EO:0007067]', description=None) | + diff --git a/mixs6/plant_product.md b/mixs6/plant_product.md new file mode 100644 index 00000000..ba48c408 --- /dev/null +++ b/mixs6/plant_product.md @@ -0,0 +1,47 @@ + +# Slot: plant_product + + +Substance produced by the plant, where the sample was obtained from + +URI: [mixs.vocab:plant_product](https://w3id.org/mixs/vocab/plant_product) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant product | +| **Mappings:** | | MIXS:0001058 | +| **Comments:** | | Expected value: product name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='xylem sap [PO:0025539]', description=None) | + diff --git a/mixs6/plant_sex.md b/mixs6/plant_sex.md new file mode 100644 index 00000000..cce0f760 --- /dev/null +++ b/mixs6/plant_sex.md @@ -0,0 +1,47 @@ + +# Slot: plant_sex + + +Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + +URI: [mixs.vocab:plant_sex](https://w3id.org/mixs/vocab/plant_sex) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant sex | +| **Mappings:** | | MIXS:0001059 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='Hermaphroditic', description=None) | + diff --git a/mixs6/plant_struc.md b/mixs6/plant_struc.md new file mode 100644 index 00000000..4e325177 --- /dev/null +++ b/mixs6/plant_struc.md @@ -0,0 +1,47 @@ + +# Slot: plant_struc + + +Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + +URI: [mixs.vocab:plant_struc](https://w3id.org/mixs/vocab/plant_struc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant structure | +| **Mappings:** | | MIXS:0001060 | +| **Comments:** | | Expected value: PO | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='epidermis [PO:0005679]', description=None) | + diff --git a/mixs6/ploidy.md b/mixs6/ploidy.md new file mode 100644 index 00000000..68873a72 --- /dev/null +++ b/mixs6/ploidy.md @@ -0,0 +1,34 @@ + +# Slot: ploidy + + +The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + +URI: [mixs.vocab:ploidy](https://w3id.org/mixs/vocab/ploidy) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ploidy | +| **Comments:** | | Expected value: PATO | +| | | Position: 15.0 | +| **Examples:** | | Example(value='allopolyploidy [PATO:0001379]', description=None) | + diff --git a/mixs6/pollutants.md b/mixs6/pollutants.md new file mode 100644 index 00000000..98ad04c7 --- /dev/null +++ b/mixs6/pollutants.md @@ -0,0 +1,48 @@ + +# Slot: pollutants + + +Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + +URI: [mixs.vocab:pollutants](https://w3id.org/mixs/vocab/pollutants) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pollutants | +| **Mappings:** | | MIXS:0000107 | +| **Comments:** | | Expected value: pollutant name;measurement value | +| | | Preferred unit: gram, mole per liter, milligram per liter, microgram per cubic meter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='lead;0.15 microgram per cubic meter', description=None) | + diff --git a/mixs6/pool_dna_extracts.md b/mixs6/pool_dna_extracts.md new file mode 100644 index 00000000..019fd2aa --- /dev/null +++ b/mixs6/pool_dna_extracts.md @@ -0,0 +1,47 @@ + +# Slot: pool_dna_extracts + + +Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + +URI: [mixs.vocab:pool_dna_extracts](https://w3id.org/mixs/vocab/pool_dna_extracts) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pooling of DNA extracts (if done) | +| **Mappings:** | | MIXS:0000325 | +| **Comments:** | | Expected value: pooling status;number of pooled extracts | +| | | Occurrence: 1 | +| | | Position: 18.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='yes;5', description=None) | + diff --git a/mixs6/porosity.md b/mixs6/porosity.md new file mode 100644 index 00000000..c24b6804 --- /dev/null +++ b/mixs6/porosity.md @@ -0,0 +1,60 @@ + +# Slot: porosity + + +Porosity of deposited sediment is volume of voids divided by the total volume of sample + +URI: [mixs.vocab:porosity](https://w3id.org/mixs/vocab/porosity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | porosity | +| **Mappings:** | | MIXS:0000211 | +| **Comments:** | | Expected value: measurement value or range | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 11.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, sediment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/potassium.md b/mixs6/potassium.md new file mode 100644 index 00000000..a7e01886 --- /dev/null +++ b/mixs6/potassium.md @@ -0,0 +1,108 @@ + +# Slot: potassium + + +Concentration of potassium in the sample + +URI: [mixs.vocab:potassium](https://w3id.org/mixs/vocab/potassium) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | potassium | +| **Mappings:** | | MIXS:0000430 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 68.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='463 milligram per liter', description=None) | + diff --git a/mixs6/pour_point.md b/mixs6/pour_point.md new file mode 100644 index 00000000..b469a8f2 --- /dev/null +++ b/mixs6/pour_point.md @@ -0,0 +1,60 @@ + +# Slot: pour_point + + +Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + +URI: [mixs.vocab:pour_point](https://w3id.org/mixs/vocab/pour_point) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pour point | +| **Mappings:** | | MIXS:0000127 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 88.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/pre_treatment.md b/mixs6/pre_treatment.md new file mode 100644 index 00000000..54970036 --- /dev/null +++ b/mixs6/pre_treatment.md @@ -0,0 +1,47 @@ + +# Slot: pre_treatment + + +The process of pre-treatment removes materials that can be easily collected from the raw wastewater + +URI: [mixs.vocab:pre_treatment](https://w3id.org/mixs/vocab/pre_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pre-treatment | +| **Mappings:** | | MIXS:0000348 | +| **Comments:** | | Expected value: pre-treatment type | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/pred_genome_struc.md b/mixs6/pred_genome_struc.md new file mode 100644 index 00000000..bb7c3239 --- /dev/null +++ b/mixs6/pred_genome_struc.md @@ -0,0 +1,34 @@ + +# Slot: pred_genome_struc + + +Expected structure of the viral genome + +URI: [mixs.vocab:pred_genome_struc](https://w3id.org/mixs/vocab/pred_genome_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | predicted genome structure | +| **Comments:** | | Expected value: enumeration | +| | | Position: 85.0 | +| **Examples:** | | Example(value='non-segmented', description=None) | + diff --git a/mixs6/pred_genome_type.md b/mixs6/pred_genome_type.md new file mode 100644 index 00000000..336a1634 --- /dev/null +++ b/mixs6/pred_genome_type.md @@ -0,0 +1,34 @@ + +# Slot: pred_genome_type + + +Type of genome predicted for the UViG + +URI: [mixs.vocab:pred_genome_type](https://w3id.org/mixs/vocab/pred_genome_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | predicted genome type | +| **Comments:** | | Expected value: enumeration | +| | | Position: 84.0 | +| **Examples:** | | Example(value='dsDNA', description=None) | + diff --git a/mixs6/pregnancy.md b/mixs6/pregnancy.md new file mode 100644 index 00000000..e43f2ff7 --- /dev/null +++ b/mixs6/pregnancy.md @@ -0,0 +1,47 @@ + +# Slot: pregnancy + + +Date due of pregnancy + +URI: [mixs.vocab:pregnancy](https://w3id.org/mixs/vocab/pregnancy) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pregnancy | +| **Mappings:** | | MIXS:0000966 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 3.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/pres_animal.md b/mixs6/pres_animal.md new file mode 100644 index 00000000..42079c46 --- /dev/null +++ b/mixs6/pres_animal.md @@ -0,0 +1,47 @@ + +# Slot: pres_animal + + +The number and type of animals present in the sampling space + +URI: [mixs.vocab:pres_animal](https://w3id.org/mixs/vocab/pres_animal) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | presence of pets, animals, or insects | +| **Mappings:** | | MIXS:0000819 | +| **Comments:** | | Expected value: enumeration;count | +| | | Occurrence: 1 | +| | | Position: 99.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='cat;5', description=None) | + diff --git a/mixs6/pressure.md b/mixs6/pressure.md new file mode 100644 index 00000000..e2cc2d67 --- /dev/null +++ b/mixs6/pressure.md @@ -0,0 +1,108 @@ + +# Slot: pressure + + +Pressure to which the sample is subject to, in atmospheres + +URI: [mixs.vocab:pressure](https://w3id.org/mixs/vocab/pressure) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pressure | +| **Mappings:** | | MIXS:0000412 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: atmosphere | +| | | Occurrence: 1 | +| | | Position: 41.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='50 atmosphere', description=None) | + diff --git a/mixs6/previous_land_use.md b/mixs6/previous_land_use.md new file mode 100644 index 00000000..e3b9785b --- /dev/null +++ b/mixs6/previous_land_use.md @@ -0,0 +1,47 @@ + +# Slot: previous_land_use + + +Previous land use and dates + +URI: [mixs.vocab:previous_land_use](https://w3id.org/mixs/vocab/previous_land_use) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/previous land use | +| **Mappings:** | | MIXS:0000315 | +| **Comments:** | | Expected value: land use name;date | +| | | Occurrence: 1 | +| | | Position: 4.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/previous_land_use_meth.md b/mixs6/previous_land_use_meth.md new file mode 100644 index 00000000..118a739e --- /dev/null +++ b/mixs6/previous_land_use_meth.md @@ -0,0 +1,47 @@ + +# Slot: previous_land_use_meth + + +Reference or method used in determining previous land use and dates + +URI: [mixs.vocab:previous_land_use_meth](https://w3id.org/mixs/vocab/previous_land_use_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/previous land use method | +| **Mappings:** | | MIXS:0000316 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 5.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/primary_prod.md b/mixs6/primary_prod.md new file mode 100644 index 00000000..a03e2452 --- /dev/null +++ b/mixs6/primary_prod.md @@ -0,0 +1,48 @@ + +# Slot: primary_prod + + +Measurement of primary production, generally measured as isotope uptake + +URI: [mixs.vocab:primary_prod](https://w3id.org/mixs/vocab/primary_prod) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | primary production | +| **Mappings:** | | MIXS:0000728 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter per day, gram per square meter per day | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='100 milligram per cubic meter per day', description=None) | + diff --git a/mixs6/primary_treatment.md b/mixs6/primary_treatment.md new file mode 100644 index 00000000..3405cdf7 --- /dev/null +++ b/mixs6/primary_treatment.md @@ -0,0 +1,47 @@ + +# Slot: primary_treatment + + +The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + +URI: [mixs.vocab:primary_treatment](https://w3id.org/mixs/vocab/primary_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | primary treatment | +| **Mappings:** | | MIXS:0000349 | +| **Comments:** | | Expected value: primary treatment type | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/prod_rate.md b/mixs6/prod_rate.md new file mode 100644 index 00000000..5b721354 --- /dev/null +++ b/mixs6/prod_rate.md @@ -0,0 +1,48 @@ + +# Slot: prod_rate + + +Oil and/or gas production rates per well (e.g. 524 m3 / day) + +URI: [mixs.vocab:prod_rate](https://w3id.org/mixs/vocab/prod_rate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | production rate | +| **Mappings:** | | MIXS:0000452 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per day | +| | | Occurrence: 1 | +| | | Position: 24.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/prod_start_date.md b/mixs6/prod_start_date.md new file mode 100644 index 00000000..4b8f32a5 --- /dev/null +++ b/mixs6/prod_start_date.md @@ -0,0 +1,47 @@ + +# Slot: prod_start_date + + +Date of field's first production + +URI: [mixs.vocab:prod_start_date](https://w3id.org/mixs/vocab/prod_start_date) + + +## Domain and Range + +None -> OPT [Date](types/Date.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | production start date | +| **Mappings:** | | MIXS:0001008 | +| **Comments:** | | Expected value: timestamp | +| | | Occurrence: 1 | +| | | Position: 23.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/profile_position.md b/mixs6/profile_position.md new file mode 100644 index 00000000..4791bf93 --- /dev/null +++ b/mixs6/profile_position.md @@ -0,0 +1,47 @@ + +# Slot: profile_position + + +Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + +URI: [mixs.vocab:profile_position](https://w3id.org/mixs/vocab/profile_position) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | profile position | +| **Mappings:** | | MIXS:0001084 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 33.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='summit', description=None) | + diff --git a/mixs6/project_name.md b/mixs6/project_name.md new file mode 100644 index 00000000..14a810dd --- /dev/null +++ b/mixs6/project_name.md @@ -0,0 +1,44 @@ + +# Slot: project_name + + +Name of the project within which the sequencing was organized + +URI: [mixs.vocab:project_name](https://w3id.org/mixs/vocab/project_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + * [ME➞project_name](ME_project_name.md) + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) + * [MIGS org➞project_name](MIGS_org_project_name.md) + * [MIGS plant➞project_name](MIGS_plant_project_name.md) + * [MIGS virus➞project_name](MIGS_virus_project_name.md) + * [MIMAG➞project_name](MIMAG_project_name.md) + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) + * [MISAG➞project_name](MISAG_project_name.md) + * [MIUVIG➞project_name](MIUVIG_project_name.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | project name | +| **Comments:** | | Position: 3.0 | +| | | This field is used in all packages | +| **Examples:** | | Example(value='Forest soil metagenome', description=None) | + diff --git a/mixs6/propagation.md b/mixs6/propagation.md new file mode 100644 index 00000000..6792bfb7 --- /dev/null +++ b/mixs6/propagation.md @@ -0,0 +1,37 @@ + +# Slot: propagation + + +This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + +URI: [mixs.vocab:propagation](https://w3id.org/mixs/vocab/propagation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) + * [MIGS plant➞propagation](MIGS_plant_propagation.md) + * [MIGS virus➞propagation](MIGS_virus_propagation.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | propagation | +| **Comments:** | | Expected value: for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual | +| | | Position: 27.0 | +| **Examples:** | | Example(value='lytic', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/88 | + diff --git a/mixs6/pulmonary_disord.md b/mixs6/pulmonary_disord.md new file mode 100644 index 00000000..1a8a19be --- /dev/null +++ b/mixs6/pulmonary_disord.md @@ -0,0 +1,47 @@ + +# Slot: pulmonary_disord + + +History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + +URI: [mixs.vocab:pulmonary_disord](https://w3id.org/mixs/vocab/pulmonary_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | lung/pulmonary disorder | +| **Mappings:** | | MIXS:0000269 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 30.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/quad_pos.md b/mixs6/quad_pos.md new file mode 100644 index 00000000..f18d908d --- /dev/null +++ b/mixs6/quad_pos.md @@ -0,0 +1,47 @@ + +# Slot: quad_pos + + +The quadrant position of the sampling room within the building + +URI: [mixs.vocab:quad_pos](https://w3id.org/mixs/vocab/quad_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | quadrant position | +| **Mappings:** | | MIXS:0000820 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 100.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='West side', description=None) | + diff --git a/mixs6/quantityValue__has_numeric_value.md b/mixs6/quantityValue__has_numeric_value.md new file mode 100644 index 00000000..e6e8c1df --- /dev/null +++ b/mixs6/quantityValue__has_numeric_value.md @@ -0,0 +1,22 @@ + +# Slot: quantityValue__has_numeric_value + + + + +URI: [mixs.vocab:quantityValue__has_numeric_value](https://w3id.org/mixs/vocab/quantityValue__has_numeric_value) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + +## Children + + +## Used by + + * [QuantityValue](QuantityValue.md) diff --git a/mixs6/quantityValue__has_raw_value.md b/mixs6/quantityValue__has_raw_value.md new file mode 100644 index 00000000..978be9b3 --- /dev/null +++ b/mixs6/quantityValue__has_raw_value.md @@ -0,0 +1,22 @@ + +# Slot: quantityValue__has_raw_value + + + + +URI: [mixs.vocab:quantityValue__has_raw_value](https://w3id.org/mixs/vocab/quantityValue__has_raw_value) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + +## Used by + + * [QuantityValue](QuantityValue.md) diff --git a/mixs6/quantityValue__has_unit.md b/mixs6/quantityValue__has_unit.md new file mode 100644 index 00000000..edcf5854 --- /dev/null +++ b/mixs6/quantityValue__has_unit.md @@ -0,0 +1,22 @@ + +# Slot: quantityValue__has_unit + + +Example "m" + +URI: [mixs.vocab:quantityValue__has_unit](https://w3id.org/mixs/vocab/quantityValue__has_unit) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + +## Used by + + * [QuantityValue](QuantityValue.md) diff --git a/mixs6/radiation_regm.md b/mixs6/radiation_regm.md new file mode 100644 index 00000000..6ff5351e --- /dev/null +++ b/mixs6/radiation_regm.md @@ -0,0 +1,48 @@ + +# Slot: radiation_regm + + +Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + +URI: [mixs.vocab:radiation_regm](https://w3id.org/mixs/vocab/radiation_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | radiation regimen | +| **Mappings:** | | MIXS:0000575 | +| **Comments:** | | Expected value: radiation type name;radiation amount;treatment interval and duration | +| | | Preferred unit: rad, gray | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/rainfall_regm.md b/mixs6/rainfall_regm.md new file mode 100644 index 00000000..68dcaaac --- /dev/null +++ b/mixs6/rainfall_regm.md @@ -0,0 +1,48 @@ + +# Slot: rainfall_regm + + +Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:rainfall_regm](https://w3id.org/mixs/vocab/rainfall_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rainfall regimen | +| **Mappings:** | | MIXS:0000576 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Preferred unit: millimeter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/reactor_type.md b/mixs6/reactor_type.md new file mode 100644 index 00000000..ecbb3dc5 --- /dev/null +++ b/mixs6/reactor_type.md @@ -0,0 +1,47 @@ + +# Slot: reactor_type + + +Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + +URI: [mixs.vocab:reactor_type](https://w3id.org/mixs/vocab/reactor_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reactor type | +| **Mappings:** | | MIXS:0000350 | +| **Comments:** | | Expected value: reactor type name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/reassembly_bin.md b/mixs6/reassembly_bin.md new file mode 100644 index 00000000..2d11a282 --- /dev/null +++ b/mixs6/reassembly_bin.md @@ -0,0 +1,35 @@ + +# Slot: reassembly_bin + + +Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + +URI: [mixs.vocab:reassembly_bin](https://w3id.org/mixs/vocab/reassembly_bin) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reassembly post binning | +| **Comments:** | | Expected value: boolean | +| | | Position: 81.0 | +| **Examples:** | | Example(value='no', description=None) | + diff --git a/mixs6/redox_potential.md b/mixs6/redox_potential.md new file mode 100644 index 00000000..d6f5b81b --- /dev/null +++ b/mixs6/redox_potential.md @@ -0,0 +1,72 @@ + +# Slot: redox_potential + + +Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + +URI: [mixs.vocab:redox_potential](https://w3id.org/mixs/vocab/redox_potential) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | redox potential | +| **Mappings:** | | MIXS:0000182 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millivolt | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='300 millivolt', description=None) | + diff --git a/mixs6/ref_biomaterial.md b/mixs6/ref_biomaterial.md new file mode 100644 index 00000000..dfdce5b5 --- /dev/null +++ b/mixs6/ref_biomaterial.md @@ -0,0 +1,42 @@ + +# Slot: ref_biomaterial + + +Primary publication if isolated before genome publication; otherwise, primary genome report + +URI: [mixs.vocab:ref_biomaterial](https://w3id.org/mixs/vocab/ref_biomaterial) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reference for biomaterial | +| **Comments:** | | Expected value: PMID, DOI or URL | +| | | Position: 19.0 | +| **Examples:** | | Example(value='doi:10.1016/j.syapm.2018.01.009', description=None) | + diff --git a/mixs6/ref_db.md b/mixs6/ref_db.md new file mode 100644 index 00000000..cb7bccd7 --- /dev/null +++ b/mixs6/ref_db.md @@ -0,0 +1,42 @@ + +# Slot: ref_db + + +List of database(s) used for ORF annotation, along with version number and reference to website or publication + +URI: [mixs.vocab:ref_db](https://w3id.org/mixs/vocab/ref_db) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞ref_db](ME_ref_db.md) + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) + * [MIGS org➞ref_db](MIGS_org_ref_db.md) + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) + * [MIMAG➞ref_db](MIMAG_ref_db.md) + * [MISAG➞ref_db](MISAG_ref_db.md) + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reference database(s) | +| **Comments:** | | Expected value: names, versions, and references of databases | +| | | Position: 60.0 | +| **Examples:** | | Example(value='pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975', description=None) | + diff --git a/mixs6/rel_air_humidity.md b/mixs6/rel_air_humidity.md new file mode 100644 index 00000000..5669b061 --- /dev/null +++ b/mixs6/rel_air_humidity.md @@ -0,0 +1,48 @@ + +# Slot: rel_air_humidity + + +Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + +URI: [mixs.vocab:rel_air_humidity](https://w3id.org/mixs/vocab/rel_air_humidity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relative air humidity | +| **Mappings:** | | MIXS:0000121 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 3.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='80%', description=None) | + diff --git a/mixs6/rel_humidity_out.md b/mixs6/rel_humidity_out.md new file mode 100644 index 00000000..8257dc63 --- /dev/null +++ b/mixs6/rel_humidity_out.md @@ -0,0 +1,48 @@ + +# Slot: rel_humidity_out + + +The recorded outside relative humidity value at the time of sampling + +URI: [mixs.vocab:rel_humidity_out](https://w3id.org/mixs/vocab/rel_humidity_out) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | outside relative humidity | +| **Mappings:** | | MIXS:0000188 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram of air, kilogram of air | +| | | Occurrence: 1 | +| | | Position: 98.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='12 per kilogram of air', description=None) | + diff --git a/mixs6/rel_samp_loc.md b/mixs6/rel_samp_loc.md new file mode 100644 index 00000000..bf4a0cea --- /dev/null +++ b/mixs6/rel_samp_loc.md @@ -0,0 +1,47 @@ + +# Slot: rel_samp_loc + + +The sampling location within the train car + +URI: [mixs.vocab:rel_samp_loc](https://w3id.org/mixs/vocab/rel_samp_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relative sampling location | +| **Mappings:** | | MIXS:0000821 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 101.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='center of car', description=None) | + diff --git a/mixs6/rel_to_oxygen.md b/mixs6/rel_to_oxygen.md new file mode 100644 index 00000000..3d70b856 --- /dev/null +++ b/mixs6/rel_to_oxygen.md @@ -0,0 +1,39 @@ + +# Slot: rel_to_oxygen + + +Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + +URI: [mixs.vocab:rel_to_oxygen](https://w3id.org/mixs/vocab/rel_to_oxygen) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relationship to oxygen | +| **Comments:** | | Expected value: enumeration | +| | | Position: 29.0 | +| **Examples:** | | Example(value='aerobe', description=None) | + diff --git a/mixs6/reservoir.md b/mixs6/reservoir.md new file mode 100644 index 00000000..55b512e1 --- /dev/null +++ b/mixs6/reservoir.md @@ -0,0 +1,59 @@ + +# Slot: reservoir + + +Name of the reservoir (e.g. Carapebus) + +URI: [mixs.vocab:reservoir](https://w3id.org/mixs/vocab/reservoir) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reservoir name | +| **Mappings:** | | MIXS:0000303 | +| **Comments:** | | Expected value: name | +| | | Occurrence: 1 | +| | | Position: 5.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/resins_pc.md b/mixs6/resins_pc.md new file mode 100644 index 00000000..10368d39 --- /dev/null +++ b/mixs6/resins_pc.md @@ -0,0 +1,60 @@ + +# Slot: resins_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:resins_pc](https://w3id.org/mixs/vocab/resins_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | resins wt% | +| **Mappings:** | | MIXS:0000134 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 91.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/resp_part_matter.md b/mixs6/resp_part_matter.md new file mode 100644 index 00000000..5ea24cf9 --- /dev/null +++ b/mixs6/resp_part_matter.md @@ -0,0 +1,48 @@ + +# Slot: resp_part_matter + + +Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + +URI: [mixs.vocab:resp_part_matter](https://w3id.org/mixs/vocab/resp_part_matter) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | respirable particulate matter | +| **Mappings:** | | MIXS:0000108 | +| **Comments:** | | Expected value: particulate matter name;measurement value | +| | | Preferred unit: microgram per cubic meter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='PM2.5;10 microgram per cubic meter', description=None) | + diff --git a/mixs6/room_air_exch_rate.md b/mixs6/room_air_exch_rate.md new file mode 100644 index 00000000..3526c730 --- /dev/null +++ b/mixs6/room_air_exch_rate.md @@ -0,0 +1,48 @@ + +# Slot: room_air_exch_rate + + +The rate at which outside air replaces indoor air in a given space + +URI: [mixs.vocab:room_air_exch_rate](https://w3id.org/mixs/vocab/room_air_exch_rate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room air exchange rate | +| **Mappings:** | | MIXS:0000169 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: liter per hour | +| | | Occurrence: 1 | +| | | Position: 102.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_architec_element.md b/mixs6/room_architec_element.md new file mode 100644 index 00000000..2afa9c45 --- /dev/null +++ b/mixs6/room_architec_element.md @@ -0,0 +1,47 @@ + +# Slot: room_architec_element + + +The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + +URI: [mixs.vocab:room_architec_element](https://w3id.org/mixs/vocab/room_architec_element) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room architectural elements | +| **Mappings:** | | MIXS:0000233 | +| **Comments:** | | Expected value: free text | +| | | Occurrence: 1 | +| | | Position: 103.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_condt.md b/mixs6/room_condt.md new file mode 100644 index 00000000..418604e9 --- /dev/null +++ b/mixs6/room_condt.md @@ -0,0 +1,47 @@ + +# Slot: room_condt + + +The condition of the room at the time of sampling + +URI: [mixs.vocab:room_condt](https://w3id.org/mixs/vocab/room_condt) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room condition | +| **Mappings:** | | MIXS:0000822 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 104.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/room_connected.md b/mixs6/room_connected.md new file mode 100644 index 00000000..e38a332b --- /dev/null +++ b/mixs6/room_connected.md @@ -0,0 +1,47 @@ + +# Slot: room_connected + + +List of rooms connected to the sampling room by a doorway + +URI: [mixs.vocab:room_connected](https://w3id.org/mixs/vocab/room_connected) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms connected by a doorway | +| **Mappings:** | | MIXS:0000826 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 116.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='office', description=None) | + diff --git a/mixs6/room_count.md b/mixs6/room_count.md new file mode 100644 index 00000000..c830e33c --- /dev/null +++ b/mixs6/room_count.md @@ -0,0 +1,47 @@ + +# Slot: room_count + + +The total count of rooms in the built structure including all room types + +URI: [mixs.vocab:room_count](https://w3id.org/mixs/vocab/room_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room count | +| **Mappings:** | | MIXS:0000234 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 105.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_dim.md b/mixs6/room_dim.md new file mode 100644 index 00000000..60499d0e --- /dev/null +++ b/mixs6/room_dim.md @@ -0,0 +1,48 @@ + +# Slot: room_dim + + +The length, width and height of sampling room + +URI: [mixs.vocab:room_dim](https://w3id.org/mixs/vocab/room_dim) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room dimensions | +| **Mappings:** | | MIXS:0000192 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 106.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_door_dist.md b/mixs6/room_door_dist.md new file mode 100644 index 00000000..2c4fa128 --- /dev/null +++ b/mixs6/room_door_dist.md @@ -0,0 +1,48 @@ + +# Slot: room_door_dist + + +Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + +URI: [mixs.vocab:room_door_dist](https://w3id.org/mixs/vocab/room_door_dist) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room door distance | +| **Mappings:** | | MIXS:0000193 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 107.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_door_share.md b/mixs6/room_door_share.md new file mode 100644 index 00000000..8698c60f --- /dev/null +++ b/mixs6/room_door_share.md @@ -0,0 +1,47 @@ + +# Slot: room_door_share + + +List of room(s) (room number, room name) sharing a door with the sampling room + +URI: [mixs.vocab:room_door_share](https://w3id.org/mixs/vocab/room_door_share) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms that share a door with sampling room | +| **Mappings:** | | MIXS:0000242 | +| **Comments:** | | Expected value: room name;room number | +| | | Occurrence: 1 | +| | | Position: 118.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_hallway.md b/mixs6/room_hallway.md new file mode 100644 index 00000000..4695667b --- /dev/null +++ b/mixs6/room_hallway.md @@ -0,0 +1,47 @@ + +# Slot: room_hallway + + +List of room(s) (room number, room name) located in the same hallway as sampling room + +URI: [mixs.vocab:room_hallway](https://w3id.org/mixs/vocab/room_hallway) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms that are on the same hallway | +| **Mappings:** | | MIXS:0000238 | +| **Comments:** | | Expected value: room name;room number | +| | | Occurrence: 1 | +| | | Position: 117.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_loc.md b/mixs6/room_loc.md new file mode 100644 index 00000000..9e06e0d7 --- /dev/null +++ b/mixs6/room_loc.md @@ -0,0 +1,47 @@ + +# Slot: room_loc + + +The position of the room within the building + +URI: [mixs.vocab:room_loc](https://w3id.org/mixs/vocab/room_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room location in building | +| **Mappings:** | | MIXS:0000823 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 108.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='interior room', description=None) | + diff --git a/mixs6/room_moist_damage_hist.md b/mixs6/room_moist_damage_hist.md new file mode 100644 index 00000000..1e061fb3 --- /dev/null +++ b/mixs6/room_moist_damage_hist.md @@ -0,0 +1,47 @@ + +# Slot: room_moist_damage_hist + + +The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + +URI: [mixs.vocab:room_moist_damage_hist](https://w3id.org/mixs/vocab/room_moist_damage_hist) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room moisture damage or mold history | +| **Mappings:** | | MIXS:0000235 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 109.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_net_area.md b/mixs6/room_net_area.md new file mode 100644 index 00000000..587b1a3b --- /dev/null +++ b/mixs6/room_net_area.md @@ -0,0 +1,48 @@ + +# Slot: room_net_area + + +The net floor area of sampling room. Net area excludes wall thicknesses + +URI: [mixs.vocab:room_net_area](https://w3id.org/mixs/vocab/room_net_area) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room net area | +| **Mappings:** | | MIXS:0000194 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square feet, square meter | +| | | Occurrence: 1 | +| | | Position: 110.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_occup.md b/mixs6/room_occup.md new file mode 100644 index 00000000..4705acef --- /dev/null +++ b/mixs6/room_occup.md @@ -0,0 +1,47 @@ + +# Slot: room_occup + + +Count of room occupancy at time of sampling + +URI: [mixs.vocab:room_occup](https://w3id.org/mixs/vocab/room_occup) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room occupancy | +| **Mappings:** | | MIXS:0000236 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 111.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_samp_pos.md b/mixs6/room_samp_pos.md new file mode 100644 index 00000000..d04a0d62 --- /dev/null +++ b/mixs6/room_samp_pos.md @@ -0,0 +1,47 @@ + +# Slot: room_samp_pos + + +The horizontal sampling position in the room relative to architectural elements + +URI: [mixs.vocab:room_samp_pos](https://w3id.org/mixs/vocab/room_samp_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room sampling position | +| **Mappings:** | | MIXS:0000824 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 112.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='south corner', description=None) | + diff --git a/mixs6/room_type.md b/mixs6/room_type.md new file mode 100644 index 00000000..b15925fd --- /dev/null +++ b/mixs6/room_type.md @@ -0,0 +1,47 @@ + +# Slot: room_type + + +The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + +URI: [mixs.vocab:room_type](https://w3id.org/mixs/vocab/room_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room type | +| **Mappings:** | | MIXS:0000825 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 113.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='bathroom', description=None) | + diff --git a/mixs6/room_vol.md b/mixs6/room_vol.md new file mode 100644 index 00000000..31a0849d --- /dev/null +++ b/mixs6/room_vol.md @@ -0,0 +1,48 @@ + +# Slot: room_vol + + +Volume of sampling room + +URI: [mixs.vocab:room_vol](https://w3id.org/mixs/vocab/room_vol) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room volume | +| **Mappings:** | | MIXS:0000195 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic feet, cubic meter | +| | | Occurrence: 1 | +| | | Position: 114.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_wall_share.md b/mixs6/room_wall_share.md new file mode 100644 index 00000000..bcaab353 --- /dev/null +++ b/mixs6/room_wall_share.md @@ -0,0 +1,47 @@ + +# Slot: room_wall_share + + +List of room(s) (room number, room name) sharing a wall with the sampling room + +URI: [mixs.vocab:room_wall_share](https://w3id.org/mixs/vocab/room_wall_share) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms that share a wall with sampling room | +| **Mappings:** | | MIXS:0000243 | +| **Comments:** | | Expected value: room name;room number | +| | | Occurrence: 1 | +| | | Position: 119.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_window_count.md b/mixs6/room_window_count.md new file mode 100644 index 00000000..6cd875de --- /dev/null +++ b/mixs6/room_window_count.md @@ -0,0 +1,47 @@ + +# Slot: room_window_count + + +Number of windows in the room + +URI: [mixs.vocab:room_window_count](https://w3id.org/mixs/vocab/room_window_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room window count | +| **Mappings:** | | MIXS:0000237 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 115.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/root_cond.md b/mixs6/root_cond.md new file mode 100644 index 00000000..f2511bbb --- /dev/null +++ b/mixs6/root_cond.md @@ -0,0 +1,47 @@ + +# Slot: root_cond + + +Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + +URI: [mixs.vocab:root_cond](https://w3id.org/mixs/vocab/root_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting conditions | +| **Mappings:** | | MIXS:0001061 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='http://himedialabs.com/TD/PT158.pdf', description=None) | + diff --git a/mixs6/root_med_carbon.md b/mixs6/root_med_carbon.md new file mode 100644 index 00000000..b714e48d --- /dev/null +++ b/mixs6/root_med_carbon.md @@ -0,0 +1,48 @@ + +# Slot: root_med_carbon + + +Source of organic carbon in the culture rooting medium; e.g. sucrose. + +URI: [mixs.vocab:root_med_carbon](https://w3id.org/mixs/vocab/root_med_carbon) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium carbon | +| **Mappings:** | | MIXS:0000577 | +| **Comments:** | | Expected value: carbon source name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='sucrose', description=None) | + diff --git a/mixs6/root_med_macronutr.md b/mixs6/root_med_macronutr.md new file mode 100644 index 00000000..12b15365 --- /dev/null +++ b/mixs6/root_med_macronutr.md @@ -0,0 +1,48 @@ + +# Slot: root_med_macronutr + + +Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + +URI: [mixs.vocab:root_med_macronutr](https://w3id.org/mixs/vocab/root_med_macronutr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium macronutrients | +| **Mappings:** | | MIXS:0000578 | +| **Comments:** | | Expected value: macronutrient name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='KH2PO4;170¬†milligram per liter', description=None) | + diff --git a/mixs6/root_med_micronutr.md b/mixs6/root_med_micronutr.md new file mode 100644 index 00000000..f7e89093 --- /dev/null +++ b/mixs6/root_med_micronutr.md @@ -0,0 +1,48 @@ + +# Slot: root_med_micronutr + + +Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + +URI: [mixs.vocab:root_med_micronutr](https://w3id.org/mixs/vocab/root_med_micronutr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium micronutrients | +| **Mappings:** | | MIXS:0000579 | +| **Comments:** | | Expected value: micronutrient name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='H3BO3;6.2¬†milligram per liter', description=None) | + diff --git a/mixs6/root_med_ph.md b/mixs6/root_med_ph.md new file mode 100644 index 00000000..9af9c472 --- /dev/null +++ b/mixs6/root_med_ph.md @@ -0,0 +1,47 @@ + +# Slot: root_med_ph + + +pH measurement of the culture rooting medium; e.g. 5.5. + +URI: [mixs.vocab:root_med_ph](https://w3id.org/mixs/vocab/root_med_ph) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium pH | +| **Mappings:** | | MIXS:0001062 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='7.5', description=None) | + diff --git a/mixs6/root_med_regl.md b/mixs6/root_med_regl.md new file mode 100644 index 00000000..0fc51c79 --- /dev/null +++ b/mixs6/root_med_regl.md @@ -0,0 +1,48 @@ + +# Slot: root_med_regl + + +Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + +URI: [mixs.vocab:root_med_regl](https://w3id.org/mixs/vocab/root_med_regl) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium regulators | +| **Mappings:** | | MIXS:0000581 | +| **Comments:** | | Expected value: regulator name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='abscisic acid;0.75 milligram per liter', description=None) | + diff --git a/mixs6/root_med_solid.md b/mixs6/root_med_solid.md new file mode 100644 index 00000000..1194f84f --- /dev/null +++ b/mixs6/root_med_solid.md @@ -0,0 +1,47 @@ + +# Slot: root_med_solid + + +Specification of the solidifying agent in the culture rooting medium; e.g. agar. + +URI: [mixs.vocab:root_med_solid](https://w3id.org/mixs/vocab/root_med_solid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium solidifier | +| **Mappings:** | | MIXS:0001063 | +| **Comments:** | | Expected value: name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='agar', description=None) | + diff --git a/mixs6/root_med_suppl.md b/mixs6/root_med_suppl.md new file mode 100644 index 00000000..d1240766 --- /dev/null +++ b/mixs6/root_med_suppl.md @@ -0,0 +1,48 @@ + +# Slot: root_med_suppl + + +Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + +URI: [mixs.vocab:root_med_suppl](https://w3id.org/mixs/vocab/root_med_suppl) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium organic supplements | +| **Mappings:** | | MIXS:0000580 | +| **Comments:** | | Expected value: supplement name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='nicotinic acid;0.5 milligram per liter', description=None) | + diff --git a/mixs6/salinity.md b/mixs6/salinity.md new file mode 100644 index 00000000..5e0bf704 --- /dev/null +++ b/mixs6/salinity.md @@ -0,0 +1,84 @@ + +# Slot: salinity + + +Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + +URI: [mixs.vocab:salinity](https://w3id.org/mixs/vocab/salinity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | salinity | +| **Mappings:** | | MIXS:0000183 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: practical salinity unit, percentage | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='25 practical salinity unit', description=None) | + diff --git a/mixs6/salinity_meth.md b/mixs6/salinity_meth.md new file mode 100644 index 00000000..6ed377b3 --- /dev/null +++ b/mixs6/salinity_meth.md @@ -0,0 +1,47 @@ + +# Slot: salinity_meth + + +Reference or method used in determining salinity + +URI: [mixs.vocab:salinity_meth](https://w3id.org/mixs/vocab/salinity_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/salinity method | +| **Mappings:** | | MIXS:0000341 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 47.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/salt_regm.md b/mixs6/salt_regm.md new file mode 100644 index 00000000..fe5d387b --- /dev/null +++ b/mixs6/salt_regm.md @@ -0,0 +1,48 @@ + +# Slot: salt_regm + + +Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + +URI: [mixs.vocab:salt_regm](https://w3id.org/mixs/vocab/salt_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | salt regimen | +| **Mappings:** | | MIXS:0000582 | +| **Comments:** | | Expected value: salt name;salt amount;treatment interval and duration | +| | | Preferred unit: gram, microgram, mole per liter, gram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/samp_capt_status.md b/mixs6/samp_capt_status.md new file mode 100644 index 00000000..1adcfbbb --- /dev/null +++ b/mixs6/samp_capt_status.md @@ -0,0 +1,59 @@ + +# Slot: samp_capt_status + + +Reason for the sample + +URI: [mixs.vocab:samp_capt_status](https://w3id.org/mixs/vocab/samp_capt_status) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample capture status | +| **Mappings:** | | MIXS:0000860 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 5.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='farm sample', description=None) | + diff --git a/mixs6/samp_collection_point.md b/mixs6/samp_collection_point.md new file mode 100644 index 00000000..ffe2f799 --- /dev/null +++ b/mixs6/samp_collection_point.md @@ -0,0 +1,47 @@ + +# Slot: samp_collection_point + + +Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_collection_point](https://w3id.org/mixs/vocab/samp_collection_point) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample collection point | +| **Mappings:** | | MIXS:0001015 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 39.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='well', description=None) | + diff --git a/mixs6/samp_dis_stage.md b/mixs6/samp_dis_stage.md new file mode 100644 index 00000000..75757c62 --- /dev/null +++ b/mixs6/samp_dis_stage.md @@ -0,0 +1,59 @@ + +# Slot: samp_dis_stage + + +Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + +URI: [mixs.vocab:samp_dis_stage](https://w3id.org/mixs/vocab/samp_dis_stage) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample disease stage | +| **Mappings:** | | MIXS:0000249 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 6.0 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='infection', description=None) | + diff --git a/mixs6/samp_floor.md b/mixs6/samp_floor.md new file mode 100644 index 00000000..932f5fdd --- /dev/null +++ b/mixs6/samp_floor.md @@ -0,0 +1,47 @@ + +# Slot: samp_floor + + +The floor of the building, where the sampling room is located + +URI: [mixs.vocab:samp_floor](https://w3id.org/mixs/vocab/samp_floor) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling floor | +| **Mappings:** | | MIXS:0000828 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 121.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='4th floor', description=None) | + diff --git a/mixs6/samp_loc_corr_rate.md b/mixs6/samp_loc_corr_rate.md new file mode 100644 index 00000000..ca96776c --- /dev/null +++ b/mixs6/samp_loc_corr_rate.md @@ -0,0 +1,48 @@ + +# Slot: samp_loc_corr_rate + + +Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + +URI: [mixs.vocab:samp_loc_corr_rate](https://w3id.org/mixs/vocab/samp_loc_corr_rate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | corrosion rate at sample location | +| **Mappings:** | | MIXS:0000136 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: millimeter per year | +| | | Occurrence: 1 | +| | | Position: 34.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_mat_process.md b/mixs6/samp_mat_process.md new file mode 100644 index 00000000..4cb31948 --- /dev/null +++ b/mixs6/samp_mat_process.md @@ -0,0 +1,44 @@ + +# Slot: samp_mat_process + + +A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. + +URI: [mixs.vocab:samp_mat_process](https://w3id.org/mixs/vocab/samp_mat_process) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞samp_mat_process](ME_samp_mat_process.md) + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample material processing | +| **Comments:** | | Expected value: text | +| | | Position: 32.0 | +| **Examples:** | | Example(value='filtering of seawater, storing samples in ethanol', description=None) | + diff --git a/mixs6/samp_md.md b/mixs6/samp_md.md new file mode 100644 index 00000000..a8f00141 --- /dev/null +++ b/mixs6/samp_md.md @@ -0,0 +1,48 @@ + +# Slot: samp_md + + +In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_md](https://w3id.org/mixs/vocab/samp_md) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample measured depth | +| **Mappings:** | | MIXS:0000413 | +| **Comments:** | | Expected value: measurement value;enumeration | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 43.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='1534 meter;MSL', description=None) | + diff --git a/mixs6/samp_preserv.md b/mixs6/samp_preserv.md new file mode 100644 index 00000000..8efb600a --- /dev/null +++ b/mixs6/samp_preserv.md @@ -0,0 +1,48 @@ + +# Slot: samp_preserv + + +Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + +URI: [mixs.vocab:samp_preserv](https://w3id.org/mixs/vocab/samp_preserv) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | preservative added to sample | +| **Mappings:** | | MIXS:0000463 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: milliliter | +| | | Occurrence: 1 | +| | | Position: 46.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_room_id.md b/mixs6/samp_room_id.md new file mode 100644 index 00000000..6b10107e --- /dev/null +++ b/mixs6/samp_room_id.md @@ -0,0 +1,47 @@ + +# Slot: samp_room_id + + +Sampling room number. This ID should be consistent with the designations on the building floor plans + +URI: [mixs.vocab:samp_room_id](https://w3id.org/mixs/vocab/samp_room_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling room ID or name | +| **Mappings:** | | MIXS:0000244 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 122.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_salinity.md b/mixs6/samp_salinity.md new file mode 100644 index 00000000..9f008837 --- /dev/null +++ b/mixs6/samp_salinity.md @@ -0,0 +1,168 @@ + +# Slot: samp_salinity + + +Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + +URI: [mixs.vocab:samp_salinity](https://w3id.org/mixs/vocab/samp_salinity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample salinity | +| **Mappings:** | | MIXS:0000109 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, practical salinity unit, percentage | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 11 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, plant-associated, wastewater_sludge | +| **Examples:** | | Example(value='1 milligram per liter', description=None) | + diff --git a/mixs6/samp_size.md b/mixs6/samp_size.md new file mode 100644 index 00000000..5b96b2b9 --- /dev/null +++ b/mixs6/samp_size.md @@ -0,0 +1,45 @@ + +# Slot: samp_size + + +Amount or size of sample (volume, mass or area) that was collected + +URI: [mixs.vocab:samp_size](https://w3id.org/mixs/vocab/samp_size) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞samp_size](ME_samp_size.md) + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) + * [MIGS org➞samp_size](MIGS_org_samp_size.md) + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) + * [MIMAG➞samp_size](MIMAG_samp_size.md) + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) + * [MISAG➞samp_size](MISAG_samp_size.md) + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amount or size of sample collected | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millliter, gram, milligram, liter | +| | | Position: 34.0 | +| **Examples:** | | Example(value='5 liter', description=None) | + diff --git a/mixs6/samp_sort_meth.md b/mixs6/samp_sort_meth.md new file mode 100644 index 00000000..9d1ceb82 --- /dev/null +++ b/mixs6/samp_sort_meth.md @@ -0,0 +1,47 @@ + +# Slot: samp_sort_meth + + +Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + +URI: [mixs.vocab:samp_sort_meth](https://w3id.org/mixs/vocab/samp_sort_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample size sorting method | +| **Mappings:** | | MIXS:0000216 | +| **Comments:** | | Expected value: description of method | +| | | Occurrence: m | +| | | Position: 22.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_store_dur.md b/mixs6/samp_store_dur.md new file mode 100644 index 00000000..8fab1347 --- /dev/null +++ b/mixs6/samp_store_dur.md @@ -0,0 +1,215 @@ + +# Slot: samp_store_dur + + +Duration for which the sample was stored + +URI: [mixs.vocab:samp_store_dur](https://w3id.org/mixs/vocab/samp_store_dur) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample storage duration | +| **Mappings:** | | MIXS:0000116 | +| **Comments:** | | Expected value: duration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='P1Y6M', description=None) | + diff --git a/mixs6/samp_store_loc.md b/mixs6/samp_store_loc.md new file mode 100644 index 00000000..ba8e2ffd --- /dev/null +++ b/mixs6/samp_store_loc.md @@ -0,0 +1,215 @@ + +# Slot: samp_store_loc + + +Location at which sample was stored, usually name of a specific freezer/room + +URI: [mixs.vocab:samp_store_loc](https://w3id.org/mixs/vocab/samp_store_loc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample storage location | +| **Mappings:** | | MIXS:0000755 | +| **Comments:** | | Expected value: location name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='Freezer no:5', description=None) | + diff --git a/mixs6/samp_store_temp.md b/mixs6/samp_store_temp.md new file mode 100644 index 00000000..b0fcafad --- /dev/null +++ b/mixs6/samp_store_temp.md @@ -0,0 +1,216 @@ + +# Slot: samp_store_temp + + +Temperature at which sample was stored, e.g. -80 degree Celsius + +URI: [mixs.vocab:samp_store_temp](https://w3id.org/mixs/vocab/samp_store_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample storage temperature | +| **Mappings:** | | MIXS:0000110 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='-80 degree Celsius', description=None) | + diff --git a/mixs6/samp_subtype.md b/mixs6/samp_subtype.md new file mode 100644 index 00000000..c8b4167e --- /dev/null +++ b/mixs6/samp_subtype.md @@ -0,0 +1,59 @@ + +# Slot: samp_subtype + + +Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_subtype](https://w3id.org/mixs/vocab/samp_subtype) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample subtype | +| **Mappings:** | | MIXS:0000999 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 38.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='biofilm', description=None) | + diff --git a/mixs6/samp_time_out.md b/mixs6/samp_time_out.md new file mode 100644 index 00000000..b9c273e1 --- /dev/null +++ b/mixs6/samp_time_out.md @@ -0,0 +1,48 @@ + +# Slot: samp_time_out + + +The recent and long term history of outside sampling + +URI: [mixs.vocab:samp_time_out](https://w3id.org/mixs/vocab/samp_time_out) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling time outside | +| **Mappings:** | | MIXS:0000196 | +| **Comments:** | | Expected value: time | +| | | Preferred unit: hour | +| | | Occurrence: 1 | +| | | Position: 123.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_transport_cond.md b/mixs6/samp_transport_cond.md new file mode 100644 index 00000000..6960df8a --- /dev/null +++ b/mixs6/samp_transport_cond.md @@ -0,0 +1,60 @@ + +# Slot: samp_transport_cond + + +Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + +URI: [mixs.vocab:samp_transport_cond](https://w3id.org/mixs/vocab/samp_transport_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample transport conditions | +| **Mappings:** | | MIXS:0000410 | +| **Comments:** | | Expected value: measurement value;measurement value | +| | | Preferred unit: days;degree Celsius | +| | | Occurrence: 1 | +| | | Position: 47.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='5 days;-20 degree Celsius', description=None) | + diff --git a/mixs6/samp_tvdss.md b/mixs6/samp_tvdss.md new file mode 100644 index 00000000..630dff66 --- /dev/null +++ b/mixs6/samp_tvdss.md @@ -0,0 +1,48 @@ + +# Slot: samp_tvdss + + +Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + +URI: [mixs.vocab:samp_tvdss](https://w3id.org/mixs/vocab/samp_tvdss) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample true vertical depth subsea | +| **Mappings:** | | MIXS:0000409 | +| **Comments:** | | Expected value: measurement value or measurement value range | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 42.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_type.md b/mixs6/samp_type.md new file mode 100644 index 00000000..9a05167c --- /dev/null +++ b/mixs6/samp_type.md @@ -0,0 +1,59 @@ + +# Slot: samp_type + + +Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_type](https://w3id.org/mixs/vocab/samp_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample type | +| **Mappings:** | | MIXS:0000998 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 37.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='solid deposit', description=None) | + diff --git a/mixs6/samp_vol_we_dna_ext.md b/mixs6/samp_vol_we_dna_ext.md new file mode 100644 index 00000000..8eb03232 --- /dev/null +++ b/mixs6/samp_vol_we_dna_ext.md @@ -0,0 +1,228 @@ + +# Slot: samp_vol_we_dna_ext + + +Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + +URI: [mixs.vocab:samp_vol_we_dna_ext](https://w3id.org/mixs/vocab/samp_vol_we_dna_ext) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample volume or weight for DNA extraction | +| **Mappings:** | | MIXS:0000111 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millliter, gram, milligram, square centimeter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 16 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='1500 milliliter', description=None) | + diff --git a/mixs6/samp_weather.md b/mixs6/samp_weather.md new file mode 100644 index 00000000..95b8d701 --- /dev/null +++ b/mixs6/samp_weather.md @@ -0,0 +1,47 @@ + +# Slot: samp_weather + + +The weather on the sampling day + +URI: [mixs.vocab:samp_weather](https://w3id.org/mixs/vocab/samp_weather) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling day weather | +| **Mappings:** | | MIXS:0000827 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 120.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='foggy', description=None) | + diff --git a/mixs6/samp_well_name.md b/mixs6/samp_well_name.md new file mode 100644 index 00000000..d175d559 --- /dev/null +++ b/mixs6/samp_well_name.md @@ -0,0 +1,59 @@ + +# Slot: samp_well_name + + +Name of the well (e.g. BXA1123) where sample was taken + +URI: [mixs.vocab:samp_well_name](https://w3id.org/mixs/vocab/samp_well_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample well name | +| **Mappings:** | | MIXS:0000296 | +| **Comments:** | | Expected value: name | +| | | Occurrence: 1 | +| | | Position: 35.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sample_collect_device.md b/mixs6/sample_collect_device.md new file mode 100644 index 00000000..d98c0341 --- /dev/null +++ b/mixs6/sample_collect_device.md @@ -0,0 +1,44 @@ + +# Slot: sample_collect_device + + +The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). + +URI: [mixs.vocab:sample_collect_device](https://w3id.org/mixs/vocab/sample_collect_device) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞sample_collect_device](ME_sample_collect_device.md) + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample collection device | +| **Comments:** | | Expected value: device name | +| | | Position: 31.0 | +| **Examples:** | | Example(value='swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]', description=None) | + diff --git a/mixs6/sample_collect_method.md b/mixs6/sample_collect_method.md new file mode 100644 index 00000000..51343740 --- /dev/null +++ b/mixs6/sample_collect_method.md @@ -0,0 +1,43 @@ + +# Slot: sample_collect_method + + +The method employed for collecting the sample. + +URI: [mixs.vocab:sample_collect_method](https://w3id.org/mixs/vocab/sample_collect_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞sample_collect_method](ME_sample_collect_method.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample collection method | +| **Comments:** | | Expected value: PMID,DOI,url , or text | +| **Examples:** | | Example(value='swabbing', description=None) | + diff --git a/mixs6/sample_name.md b/mixs6/sample_name.md new file mode 100644 index 00000000..5e47c653 --- /dev/null +++ b/mixs6/sample_name.md @@ -0,0 +1,45 @@ + +# Slot: sample_name + + +Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + +URI: [mixs.vocab:sample_name](https://w3id.org/mixs/vocab/sample_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + * [ME➞sample_name](ME_sample_name.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) + * [MIGS org➞sample_name](MIGS_org_sample_name.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) + * [MIMAG➞sample_name](MIMAG_sample_name.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) + * [MISAG➞sample_name](MISAG_sample_name.md) + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample name | +| **Comments:** | | Expected value: text | +| | | This field is used in all packages | +| **Examples:** | | Example(value='ISDsoil1', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/78 | + diff --git a/mixs6/saturates_pc.md b/mixs6/saturates_pc.md new file mode 100644 index 00000000..c9b33519 --- /dev/null +++ b/mixs6/saturates_pc.md @@ -0,0 +1,60 @@ + +# Slot: saturates_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:saturates_pc](https://w3id.org/mixs/vocab/saturates_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | saturates wt% | +| **Mappings:** | | MIXS:0000131 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 89.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/season.md b/mixs6/season.md new file mode 100644 index 00000000..80adbba6 --- /dev/null +++ b/mixs6/season.md @@ -0,0 +1,47 @@ + +# Slot: season + + +The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + +URI: [mixs.vocab:season](https://w3id.org/mixs/vocab/season) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | season | +| **Mappings:** | | MIXS:0000829 | +| **Comments:** | | Expected value: NCIT:C94729 | +| | | Occurrence: 1 | +| | | Position: 124.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='autumn [NCIT:C94733]', description=None) | + diff --git a/mixs6/season_environment.md b/mixs6/season_environment.md new file mode 100644 index 00000000..de42190f --- /dev/null +++ b/mixs6/season_environment.md @@ -0,0 +1,47 @@ + +# Slot: season_environment + + +Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + +URI: [mixs.vocab:season_environment](https://w3id.org/mixs/vocab/season_environment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | seasonal environment | +| **Mappings:** | | MIXS:0001068 | +| **Comments:** | | Expected value: seasonal environment name;treatment interval and duration | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/season_precpt.md b/mixs6/season_precpt.md new file mode 100644 index 00000000..1cd61607 --- /dev/null +++ b/mixs6/season_precpt.md @@ -0,0 +1,48 @@ + +# Slot: season_precpt + + +The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + +URI: [mixs.vocab:season_precpt](https://w3id.org/mixs/vocab/season_precpt) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean seasonal precipitation | +| **Mappings:** | | MIXS:0000645 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter | +| | | Occurrence: 1 | +| | | Position: 24.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/season_temp.md b/mixs6/season_temp.md new file mode 100644 index 00000000..0087e8db --- /dev/null +++ b/mixs6/season_temp.md @@ -0,0 +1,48 @@ + +# Slot: season_temp + + +Mean seasonal temperature + +URI: [mixs.vocab:season_temp](https://w3id.org/mixs/vocab/season_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean seasonal temperature | +| **Mappings:** | | MIXS:0000643 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 22.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='18 degree Celsius', description=None) | + diff --git a/mixs6/season_use.md b/mixs6/season_use.md new file mode 100644 index 00000000..e5f02cc7 --- /dev/null +++ b/mixs6/season_use.md @@ -0,0 +1,47 @@ + +# Slot: season_use + + +The seasons the space is occupied + +URI: [mixs.vocab:season_use](https://w3id.org/mixs/vocab/season_use) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | seasonal use | +| **Mappings:** | | MIXS:0000830 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 125.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='Winter', description=None) | + diff --git a/mixs6/secondary_treatment.md b/mixs6/secondary_treatment.md new file mode 100644 index 00000000..db1ffd28 --- /dev/null +++ b/mixs6/secondary_treatment.md @@ -0,0 +1,47 @@ + +# Slot: secondary_treatment + + +The process for substantially degrading the biological content of the sewage + +URI: [mixs.vocab:secondary_treatment](https://w3id.org/mixs/vocab/secondary_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | secondary treatment | +| **Mappings:** | | MIXS:0000351 | +| **Comments:** | | Expected value: secondary treatment type | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sediment_type.md b/mixs6/sediment_type.md new file mode 100644 index 00000000..1df30c9a --- /dev/null +++ b/mixs6/sediment_type.md @@ -0,0 +1,47 @@ + +# Slot: sediment_type + + +Information about the sediment type based on major constituents + +URI: [mixs.vocab:sediment_type](https://w3id.org/mixs/vocab/sediment_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sediment type | +| **Mappings:** | | MIXS:0001078 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: sediment | +| **Examples:** | | Example(value='biogenous', description=None) | + diff --git a/mixs6/seq_meth.md b/mixs6/seq_meth.md new file mode 100644 index 00000000..eb5719fa --- /dev/null +++ b/mixs6/seq_meth.md @@ -0,0 +1,44 @@ + +# Slot: seq_meth + + +Sequencing method used; e.g. Sanger, ABI-solid + +URI: [mixs.vocab:seq_meth](https://w3id.org/mixs/vocab/seq_meth) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞seq_meth](ME_seq_meth.md) + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) + * [MISAG➞seq_meth](MISAG_seq_meth.md) + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sequencing method | +| **Comments:** | | Expected value: enumeration | +| | | Position: 50.0 | +| **Examples:** | | Example(value='Illumina HiSeq 1500', description=None) | + diff --git a/mixs6/seq_quality_check.md b/mixs6/seq_quality_check.md new file mode 100644 index 00000000..29247655 --- /dev/null +++ b/mixs6/seq_quality_check.md @@ -0,0 +1,35 @@ + +# Slot: seq_quality_check + + +Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + +URI: [mixs.vocab:seq_quality_check](https://w3id.org/mixs/vocab/seq_quality_check) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sequence quality check | +| **Comments:** | | Expected value: none or manually edited | +| | | Position: 51.0 | +| **Examples:** | | Example(value='none', description=None) | + diff --git a/mixs6/sequencing_field.md b/mixs6/sequencing_field.md new file mode 100644 index 00000000..0d6c4d13 --- /dev/null +++ b/mixs6/sequencing_field.md @@ -0,0 +1,77 @@ + +# Slot: sequencing_field + + + + +URI: [mixs.vocab:sequencing_field](https://w3id.org/mixs/vocab/sequencing_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [adapters](adapters.md) + * [annot](annot.md) + * [assembly_name](assembly_name.md) + * [assembly_qual](assembly_qual.md) + * [assembly_software](assembly_software.md) + * [bin_param](bin_param.md) + * [bin_software](bin_software.md) + * [chimera_check](chimera_check.md) + * [compl_appr](compl_appr.md) + * [compl_score](compl_score.md) + * [compl_software](compl_software.md) + * [contam_score](contam_score.md) + * [contam_screen_input](contam_screen_input.md) + * [contam_screen_param](contam_screen_param.md) + * [decontam_software](decontam_software.md) + * [detec_type](detec_type.md) + * [feat_pred](feat_pred.md) + * [host_pred_appr](host_pred_appr.md) + * [host_pred_est_acc](host_pred_est_acc.md) + * [lib_layout](lib_layout.md) + * [lib_reads_seqd](lib_reads_seqd.md) + * [lib_screen](lib_screen.md) + * [lib_size](lib_size.md) + * [lib_vector](lib_vector.md) + * [mag_cov_software](mag_cov_software.md) + * [mid](mid.md) + * [nucl_acid_amp](nucl_acid_amp.md) + * [nucl_acid_ext](nucl_acid_ext.md) + * [number_contig](number_contig.md) + * [pcr_cond](pcr_cond.md) + * [pcr_primers](pcr_primers.md) + * [pred_genome_struc](pred_genome_struc.md) + * [pred_genome_type](pred_genome_type.md) + * [reassembly_bin](reassembly_bin.md) + * [ref_db](ref_db.md) + * [seq_meth](seq_meth.md) + * [seq_quality_check](seq_quality_check.md) + * [sim_search_meth](sim_search_meth.md) + * [single_cell_lysis_appr](single_cell_lysis_appr.md) + * [single_cell_lysis_prot](single_cell_lysis_prot.md) + * [sop](sop.md) + * [sort_tech](sort_tech.md) + * [target_gene](target_gene.md) + * [target_subfragment](target_subfragment.md) + * [tax_class](tax_class.md) + * [tax_ident](tax_ident.md) + * [trna_ext_software](trna_ext_software.md) + * [trnas](trnas.md) + * [url](url.md) + * [vir_ident_software](vir_ident_software.md) + * [votu_class_appr](votu_class_appr.md) + * [votu_db](votu_db.md) + * [votu_seq_comp_appr](votu_seq_comp_appr.md) + * [wga_amp_appr](wga_amp_appr.md) + * [wga_amp_kit](wga_amp_kit.md) + * [x_16s_recover](x_16s_recover.md) + +## Used by + diff --git a/mixs6/sewage_type.md b/mixs6/sewage_type.md new file mode 100644 index 00000000..ae42908c --- /dev/null +++ b/mixs6/sewage_type.md @@ -0,0 +1,47 @@ + +# Slot: sewage_type + + +Type of wastewater treatment plant as municipial or industrial + +URI: [mixs.vocab:sewage_type](https://w3id.org/mixs/vocab/sewage_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sewage type | +| **Mappings:** | | MIXS:0000215 | +| **Comments:** | | Expected value: sewage type name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sexual_act.md b/mixs6/sexual_act.md new file mode 100644 index 00000000..84b3719c --- /dev/null +++ b/mixs6/sexual_act.md @@ -0,0 +1,47 @@ + +# Slot: sexual_act + + +Current sexual partner and frequency of sex + +URI: [mixs.vocab:sexual_act](https://w3id.org/mixs/vocab/sexual_act) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sexual activity | +| **Mappings:** | | MIXS:0000285 | +| **Comments:** | | Expected value: partner sex;frequency | +| | | Occurrence: 1 | +| | | Position: 2.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/shading_device_cond.md b/mixs6/shading_device_cond.md new file mode 100644 index 00000000..256229ff --- /dev/null +++ b/mixs6/shading_device_cond.md @@ -0,0 +1,47 @@ + +# Slot: shading_device_cond + + +The physical condition of the shading device at the time of sampling + +URI: [mixs.vocab:shading_device_cond](https://w3id.org/mixs/vocab/shading_device_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device condition | +| **Mappings:** | | MIXS:0000831 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 126.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/shading_device_loc.md b/mixs6/shading_device_loc.md new file mode 100644 index 00000000..cae73c53 --- /dev/null +++ b/mixs6/shading_device_loc.md @@ -0,0 +1,47 @@ + +# Slot: shading_device_loc + + +The location of the shading device in relation to the built structure + +URI: [mixs.vocab:shading_device_loc](https://w3id.org/mixs/vocab/shading_device_loc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device location | +| **Mappings:** | | MIXS:0000832 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 127.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='exterior', description=None) | + diff --git a/mixs6/shading_device_mat.md b/mixs6/shading_device_mat.md new file mode 100644 index 00000000..a2140f18 --- /dev/null +++ b/mixs6/shading_device_mat.md @@ -0,0 +1,47 @@ + +# Slot: shading_device_mat + + +The material the shading device is composed of + +URI: [mixs.vocab:shading_device_mat](https://w3id.org/mixs/vocab/shading_device_mat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device material | +| **Mappings:** | | MIXS:0000245 | +| **Comments:** | | Expected value: material name | +| | | Occurrence: 1 | +| | | Position: 128.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/shading_device_type.md b/mixs6/shading_device_type.md new file mode 100644 index 00000000..61d23db3 --- /dev/null +++ b/mixs6/shading_device_type.md @@ -0,0 +1,47 @@ + +# Slot: shading_device_type + + +The type of shading device + +URI: [mixs.vocab:shading_device_type](https://w3id.org/mixs/vocab/shading_device_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device type | +| **Mappings:** | | MIXS:0000835 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 130.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='slatted aluminum awning', description=None) | + diff --git a/mixs6/shading_device_water_mold.md b/mixs6/shading_device_water_mold.md new file mode 100644 index 00000000..3a20178f --- /dev/null +++ b/mixs6/shading_device_water_mold.md @@ -0,0 +1,47 @@ + +# Slot: shading_device_water_mold + + +Signs of the presence of mold or mildew on the shading device + +URI: [mixs.vocab:shading_device_water_mold](https://w3id.org/mixs/vocab/shading_device_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device signs of water/mold | +| **Mappings:** | | MIXS:0000834 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 129.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='no presence of mold visible', description=None) | + diff --git a/mixs6/sieving.md b/mixs6/sieving.md new file mode 100644 index 00000000..42523bad --- /dev/null +++ b/mixs6/sieving.md @@ -0,0 +1,47 @@ + +# Slot: sieving + + +Collection design of pooled samples and/or sieve size and amount of sample sieved + +URI: [mixs.vocab:sieving](https://w3id.org/mixs/vocab/sieving) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | composite design/sieving (if any) | +| **Mappings:** | | MIXS:0000322 | +| **Comments:** | | Expected value: design name and/or size;amount | +| | | Occurrence: 1 | +| | | Position: 14.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/silicate.md b/mixs6/silicate.md new file mode 100644 index 00000000..2a3f5d66 --- /dev/null +++ b/mixs6/silicate.md @@ -0,0 +1,84 @@ + +# Slot: silicate + + +Concentration of silicate + +URI: [mixs.vocab:silicate](https://w3id.org/mixs/vocab/silicate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | silicate | +| **Mappings:** | | MIXS:0000184 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.05 micromole per liter', description=None) | + diff --git a/mixs6/sim_search_meth.md b/mixs6/sim_search_meth.md new file mode 100644 index 00000000..944a98a2 --- /dev/null +++ b/mixs6/sim_search_meth.md @@ -0,0 +1,42 @@ + +# Slot: sim_search_meth + + +Tool used to compare ORFs with database, along with version and cutoffs used + +URI: [mixs.vocab:sim_search_meth](https://w3id.org/mixs/vocab/sim_search_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞sim_search_meth](ME_sim_search_meth.md) + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | similarity search method | +| **Comments:** | | Expected value: names and versions of software(s), parameters used | +| | | Position: 61.0 | +| **Examples:** | | Example(value='HMMER3;3.1b2;hmmsearch, cutoff of 50 on score', description=None) | + diff --git a/mixs6/single_cell_lysis_appr.md b/mixs6/single_cell_lysis_appr.md new file mode 100644 index 00000000..adb609ee --- /dev/null +++ b/mixs6/single_cell_lysis_appr.md @@ -0,0 +1,35 @@ + +# Slot: single_cell_lysis_appr + + +Method used to free DNA from interior of the cell(s) or particle(s) + +URI: [mixs.vocab:single_cell_lysis_appr](https://w3id.org/mixs/vocab/single_cell_lysis_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | single cell or viral particle lysis approach | +| **Comments:** | | Expected value: enumeration | +| | | Position: 75.0 | +| **Examples:** | | Example(value='enzymatic', description=None) | + diff --git a/mixs6/single_cell_lysis_prot.md b/mixs6/single_cell_lysis_prot.md new file mode 100644 index 00000000..203ea700 --- /dev/null +++ b/mixs6/single_cell_lysis_prot.md @@ -0,0 +1,35 @@ + +# Slot: single_cell_lysis_prot + + +Name of the kit or standard protocol used for cell(s) or particle(s) lysis + +URI: [mixs.vocab:single_cell_lysis_prot](https://w3id.org/mixs/vocab/single_cell_lysis_prot) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | single cell or viral particle lysis kit protocol | +| **Comments:** | | Expected value: kit, protocol name | +| | | Position: 76.0 | +| **Examples:** | | Example(value='ambion single cell lysis kit', description=None) | + diff --git a/mixs6/size_frac.md b/mixs6/size_frac.md new file mode 100644 index 00000000..c82690df --- /dev/null +++ b/mixs6/size_frac.md @@ -0,0 +1,38 @@ + +# Slot: size_frac + + +Filtering pore size used in sample preparation + +URI: [mixs.vocab:size_frac](https://w3id.org/mixs/vocab/size_frac) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞size_frac](ME_size_frac.md) + * [MIMAG➞size_frac](MIMAG_size_frac.md) + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) + * [MISAG➞size_frac](MISAG_size_frac.md) + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | size fraction selected | +| **Comments:** | | Expected value: filter size value range | +| | | Position: 33.0 | +| **Examples:** | | Example(value='0-0.22 micrometer', description=None) | + diff --git a/mixs6/size_frac_low.md b/mixs6/size_frac_low.md new file mode 100644 index 00000000..7f164dd9 --- /dev/null +++ b/mixs6/size_frac_low.md @@ -0,0 +1,48 @@ + +# Slot: size_frac_low + + +Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + +URI: [mixs.vocab:size_frac_low](https://w3id.org/mixs/vocab/size_frac_low) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | size-fraction lower threshold | +| **Mappings:** | | MIXS:0000735 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: micrometer | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.2 micrometer', description=None) | + diff --git a/mixs6/size_frac_up.md b/mixs6/size_frac_up.md new file mode 100644 index 00000000..ed7dee09 --- /dev/null +++ b/mixs6/size_frac_up.md @@ -0,0 +1,48 @@ + +# Slot: size_frac_up + + +Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + +URI: [mixs.vocab:size_frac_up](https://w3id.org/mixs/vocab/size_frac_up) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | size-fraction upper threshold | +| **Mappings:** | | MIXS:0000736 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: micrometer | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='20 micrometer', description=None) | + diff --git a/mixs6/slope_aspect.md b/mixs6/slope_aspect.md new file mode 100644 index 00000000..42625811 --- /dev/null +++ b/mixs6/slope_aspect.md @@ -0,0 +1,48 @@ + +# Slot: slope_aspect + + +The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + +URI: [mixs.vocab:slope_aspect](https://w3id.org/mixs/vocab/slope_aspect) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | slope aspect | +| **Mappings:** | | MIXS:0000647 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree | +| | | Occurrence: 1 | +| | | Position: 32.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/slope_gradient.md b/mixs6/slope_gradient.md new file mode 100644 index 00000000..4833d6e2 --- /dev/null +++ b/mixs6/slope_gradient.md @@ -0,0 +1,48 @@ + +# Slot: slope_gradient + + +Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + +URI: [mixs.vocab:slope_gradient](https://w3id.org/mixs/vocab/slope_gradient) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | slope gradient | +| **Mappings:** | | MIXS:0000646 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 31.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sludge_retent_time.md b/mixs6/sludge_retent_time.md new file mode 100644 index 00000000..b6375977 --- /dev/null +++ b/mixs6/sludge_retent_time.md @@ -0,0 +1,48 @@ + +# Slot: sludge_retent_time + + +The time activated sludge remains in reactor + +URI: [mixs.vocab:sludge_retent_time](https://w3id.org/mixs/vocab/sludge_retent_time) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sludge retention time | +| **Mappings:** | | MIXS:0000669 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: hours | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/smoker.md b/mixs6/smoker.md new file mode 100644 index 00000000..9923ff4d --- /dev/null +++ b/mixs6/smoker.md @@ -0,0 +1,47 @@ + +# Slot: smoker + + +Specification of smoking status + +URI: [mixs.vocab:smoker](https://w3id.org/mixs/vocab/smoker) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | smoker | +| **Mappings:** | | MIXS:0000262 | +| **Comments:** | | Expected value: smoking status | +| | | Occurrence: 1 | +| | | Position: 17.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/sodium.md b/mixs6/sodium.md new file mode 100644 index 00000000..d45d486c --- /dev/null +++ b/mixs6/sodium.md @@ -0,0 +1,120 @@ + +# Slot: sodium + + +Sodium concentration in the sample + +URI: [mixs.vocab:sodium](https://w3id.org/mixs/vocab/sodium) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sodium | +| **Mappings:** | | MIXS:0000428 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 66.0 | +| | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='10.5 milligram per liter', description=None) | + diff --git a/mixs6/soil_type.md b/mixs6/soil_type.md new file mode 100644 index 00000000..cf2ac75d --- /dev/null +++ b/mixs6/soil_type.md @@ -0,0 +1,47 @@ + +# Slot: soil_type + + +Soil series name or other lower-level classification + +URI: [mixs.vocab:soil_type](https://w3id.org/mixs/vocab/soil_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil type | +| **Mappings:** | | MIXS:0000332 | +| **Comments:** | | Expected value: soil type name | +| | | Occurrence: 1 | +| | | Position: 29.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/soil_type_meth.md b/mixs6/soil_type_meth.md new file mode 100644 index 00000000..03c95050 --- /dev/null +++ b/mixs6/soil_type_meth.md @@ -0,0 +1,47 @@ + +# Slot: soil_type_meth + + +Reference or method used in determining soil series name or other lower-level classification + +URI: [mixs.vocab:soil_type_meth](https://w3id.org/mixs/vocab/soil_type_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil type method | +| **Mappings:** | | MIXS:0000334 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 30.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/solar_irradiance.md b/mixs6/solar_irradiance.md new file mode 100644 index 00000000..e6237175 --- /dev/null +++ b/mixs6/solar_irradiance.md @@ -0,0 +1,48 @@ + +# Slot: solar_irradiance + + +The amount of solar energy that arrives at a specific area of a surface during a specific time interval + +URI: [mixs.vocab:solar_irradiance](https://w3id.org/mixs/vocab/solar_irradiance) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | solar irradiance | +| **Mappings:** | | MIXS:0000112 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilowatts per square meter per day, ergs per square centimeter per second | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='1.36 kilowatts per square meter per day', description=None) | + diff --git a/mixs6/soluble_inorg_mat.md b/mixs6/soluble_inorg_mat.md new file mode 100644 index 00000000..928a87cd --- /dev/null +++ b/mixs6/soluble_inorg_mat.md @@ -0,0 +1,48 @@ + +# Slot: soluble_inorg_mat + + +Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + +URI: [mixs.vocab:soluble_inorg_mat](https://w3id.org/mixs/vocab/soluble_inorg_mat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soluble inorganic material | +| **Mappings:** | | MIXS:0000672 | +| **Comments:** | | Expected value: soluble inorganic material name;measurement value | +| | | Preferred unit: gram, microgram, mole per liter, gram per liter, parts per million | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/soluble_org_mat.md b/mixs6/soluble_org_mat.md new file mode 100644 index 00000000..25b97b61 --- /dev/null +++ b/mixs6/soluble_org_mat.md @@ -0,0 +1,48 @@ + +# Slot: soluble_org_mat + + +Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + +URI: [mixs.vocab:soluble_org_mat](https://w3id.org/mixs/vocab/soluble_org_mat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soluble organic material | +| **Mappings:** | | MIXS:0000673 | +| **Comments:** | | Expected value: soluble organic material name;measurement value | +| | | Preferred unit: gram, microgram, mole per liter, gram per liter, parts per million | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/soluble_react_phosp.md b/mixs6/soluble_react_phosp.md new file mode 100644 index 00000000..7ec85d5c --- /dev/null +++ b/mixs6/soluble_react_phosp.md @@ -0,0 +1,48 @@ + +# Slot: soluble_react_phosp + + +Concentration of soluble reactive phosphorus + +URI: [mixs.vocab:soluble_react_phosp](https://w3id.org/mixs/vocab/soluble_react_phosp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soluble reactive phosphorus | +| **Mappings:** | | MIXS:0000738 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.1 milligram per liter', description=None) | + diff --git a/mixs6/sop.md b/mixs6/sop.md new file mode 100644 index 00000000..1d45b831 --- /dev/null +++ b/mixs6/sop.md @@ -0,0 +1,44 @@ + +# Slot: sop + + +Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + +URI: [mixs.vocab:sop](https://w3id.org/mixs/vocab/sop) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞sop](ME_sop.md) + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) + * [MIGS org➞sop](MIGS_org_sop.md) + * [MIGS plant➞sop](MIGS_plant_sop.md) + * [MIGS virus➞sop](MIGS_virus_sop.md) + * [MIMAG➞sop](MIMAG_sop.md) + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) + * [MISAG➞sop](MISAG_sop.md) + * [MIUVIG➞sop](MIUVIG_sop.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relevant standard operating procedures | +| **Comments:** | | Expected value: reference to SOP | +| | | Position: 93.0 | +| **Examples:** | | Example(value='http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/', description=None) | + diff --git a/mixs6/sort_tech.md b/mixs6/sort_tech.md new file mode 100644 index 00000000..471f0b2c --- /dev/null +++ b/mixs6/sort_tech.md @@ -0,0 +1,35 @@ + +# Slot: sort_tech + + +Method used to sort/isolate cells or particles of interest + +URI: [mixs.vocab:sort_tech](https://w3id.org/mixs/vocab/sort_tech) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MISAG➞sort_tech](MISAG_sort_tech.md) + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sorting technology | +| **Comments:** | | Expected value: enumeration | +| | | Position: 74.0 | +| **Examples:** | | Example(value='optical manipulation', description=None) | + diff --git a/mixs6/source_mat_id.md b/mixs6/source_mat_id.md new file mode 100644 index 00000000..a0a2fd0a --- /dev/null +++ b/mixs6/source_mat_id.md @@ -0,0 +1,44 @@ + +# Slot: source_mat_id + + +A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + +URI: [mixs.vocab:source_mat_id](https://w3id.org/mixs/vocab/source_mat_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞source_mat_id](ME_source_mat_id.md) + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source material identifiers | +| **Comments:** | | Expected value: for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer | +| | | Position: 20.0 | +| **Examples:** | | Example(value='MPI012345', description=None) | + diff --git a/mixs6/source_uvig.md b/mixs6/source_uvig.md new file mode 100644 index 00000000..e38df17b --- /dev/null +++ b/mixs6/source_uvig.md @@ -0,0 +1,34 @@ + +# Slot: source_uvig + + +Type of dataset from which the UViG was obtained + +URI: [mixs.vocab:source_uvig](https://w3id.org/mixs/vocab/source_uvig) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source of UViGs | +| **Comments:** | | Expected value: enumeration | +| | | Position: 35.0 | +| **Examples:** | | Example(value='viral fraction metagenome (virome)', description=None) | + diff --git a/mixs6/space_typ_state.md b/mixs6/space_typ_state.md new file mode 100644 index 00000000..58aa901f --- /dev/null +++ b/mixs6/space_typ_state.md @@ -0,0 +1,47 @@ + +# Slot: space_typ_state + + +Customary or normal state of the space + +URI: [mixs.vocab:space_typ_state](https://w3id.org/mixs/vocab/space_typ_state) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | space typical state | +| **Mappings:** | | MIXS:0000770 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 23.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='typically occupied', description=None) | + diff --git a/mixs6/special_diet.md b/mixs6/special_diet.md new file mode 100644 index 00000000..455bd8ca --- /dev/null +++ b/mixs6/special_diet.md @@ -0,0 +1,47 @@ + +# Slot: special_diet + + +Specification of special diet; can include multiple special diets + +URI: [mixs.vocab:special_diet](https://w3id.org/mixs/vocab/special_diet) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | special diet | +| **Mappings:** | | MIXS:0000905 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 3.0 | +| | | This field is used uniquely in: human-gut | +| **Examples:** | | Example(value='other:vegan', description=None) | + diff --git a/mixs6/specific.md b/mixs6/specific.md new file mode 100644 index 00000000..4b7fcc89 --- /dev/null +++ b/mixs6/specific.md @@ -0,0 +1,47 @@ + +# Slot: specific + + +The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + +URI: [mixs.vocab:specific](https://w3id.org/mixs/vocab/specific) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | specifications | +| **Mappings:** | | MIXS:0000836 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 132.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='construction', description=None) | + diff --git a/mixs6/specific_host.md b/mixs6/specific_host.md new file mode 100644 index 00000000..d5bc01f0 --- /dev/null +++ b/mixs6/specific_host.md @@ -0,0 +1,38 @@ + +# Slot: specific_host + + +If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + +URI: [mixs.vocab:specific_host](https://w3id.org/mixs/vocab/specific_host) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | specific host | +| **Comments:** | | Expected value: host taxid, unknown, environmental | +| | | Position: 23.0 | +| **Examples:** | | Example(value='9606', description=None) | + diff --git a/mixs6/specific_humidity.md b/mixs6/specific_humidity.md new file mode 100644 index 00000000..d68077f4 --- /dev/null +++ b/mixs6/specific_humidity.md @@ -0,0 +1,48 @@ + +# Slot: specific_humidity + + +The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + +URI: [mixs.vocab:specific_humidity](https://w3id.org/mixs/vocab/specific_humidity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | specific humidity | +| **Mappings:** | | MIXS:0000214 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram of air, kilogram of air | +| | | Occurrence: 1 | +| | | Position: 131.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='15 per kilogram of air', description=None) | + diff --git a/mixs6/sr_dep_env.md b/mixs6/sr_dep_env.md new file mode 100644 index 00000000..930220a0 --- /dev/null +++ b/mixs6/sr_dep_env.md @@ -0,0 +1,47 @@ + +# Slot: sr_dep_env + + +Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_dep_env](https://w3id.org/mixs/vocab/sr_dep_env) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock depositional environment | +| **Mappings:** | | MIXS:0000996 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 21.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Marine', description=None) | + diff --git a/mixs6/sr_geol_age.md b/mixs6/sr_geol_age.md new file mode 100644 index 00000000..c0f152f2 --- /dev/null +++ b/mixs6/sr_geol_age.md @@ -0,0 +1,47 @@ + +# Slot: sr_geol_age + + +Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_geol_age](https://w3id.org/mixs/vocab/sr_geol_age) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock geological age | +| **Mappings:** | | MIXS:0000997 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 22.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Silurian', description=None) | + diff --git a/mixs6/sr_kerog_type.md b/mixs6/sr_kerog_type.md new file mode 100644 index 00000000..a8734b8f --- /dev/null +++ b/mixs6/sr_kerog_type.md @@ -0,0 +1,47 @@ + +# Slot: sr_kerog_type + + +Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_kerog_type](https://w3id.org/mixs/vocab/sr_kerog_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock kerogen type | +| **Mappings:** | | MIXS:0000994 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 19.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Type IV', description=None) | + diff --git a/mixs6/sr_lithology.md b/mixs6/sr_lithology.md new file mode 100644 index 00000000..f8cccd26 --- /dev/null +++ b/mixs6/sr_lithology.md @@ -0,0 +1,47 @@ + +# Slot: sr_lithology + + +Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_lithology](https://w3id.org/mixs/vocab/sr_lithology) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock lithology | +| **Mappings:** | | MIXS:0000995 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 20.0 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Coal', description=None) | + diff --git a/mixs6/standing_water_regm.md b/mixs6/standing_water_regm.md new file mode 100644 index 00000000..6021a42e --- /dev/null +++ b/mixs6/standing_water_regm.md @@ -0,0 +1,47 @@ + +# Slot: standing_water_regm + + +Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:standing_water_regm](https://w3id.org/mixs/vocab/standing_water_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | standing water regimen | +| **Mappings:** | | MIXS:0001069 | +| **Comments:** | | Expected value: standing water type;treatment interval and duration | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/store_cond.md b/mixs6/store_cond.md new file mode 100644 index 00000000..46c7368f --- /dev/null +++ b/mixs6/store_cond.md @@ -0,0 +1,47 @@ + +# Slot: store_cond + + +Explain how and for how long the soil sample was stored before DNA extraction + +URI: [mixs.vocab:store_cond](https://w3id.org/mixs/vocab/store_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | storage conditions (fresh/frozen/other) | +| **Mappings:** | | MIXS:0000327 | +| **Comments:** | | Expected value: storage condition type;duration | +| | | Occurrence: 1 | +| | | Position: 19.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='-20 degree Celsius freezer;P2Y10D', description=None) | + diff --git a/mixs6/study_complt_stat.md b/mixs6/study_complt_stat.md new file mode 100644 index 00000000..70416b0c --- /dev/null +++ b/mixs6/study_complt_stat.md @@ -0,0 +1,47 @@ + +# Slot: study_complt_stat + + +Specification of study completion status, if no the reason should be specified + +URI: [mixs.vocab:study_complt_stat](https://w3id.org/mixs/vocab/study_complt_stat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | study completion status | +| **Mappings:** | | MIXS:0000898 | +| **Comments:** | | Expected value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow up (4)other-specify | +| | | Occurrence: 1 | +| | | Position: 29.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='no;non-compliance', description=None) | + diff --git a/mixs6/submitted_to_insdc.md b/mixs6/submitted_to_insdc.md new file mode 100644 index 00000000..179c0b35 --- /dev/null +++ b/mixs6/submitted_to_insdc.md @@ -0,0 +1,44 @@ + +# Slot: submitted_to_insdc + + +Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + +URI: [mixs.vocab:submitted_to_insdc](https://w3id.org/mixs/vocab/submitted_to_insdc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | submitted to insdc | +| **Comments:** | | Expected value: boolean | +| | | Position: 1.0 | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/subspecf_gen_lin.md b/mixs6/subspecf_gen_lin.md new file mode 100644 index 00000000..63f13ed7 --- /dev/null +++ b/mixs6/subspecf_gen_lin.md @@ -0,0 +1,39 @@ + +# Slot: subspecf_gen_lin + + +This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + +URI: [mixs.vocab:subspecf_gen_lin](https://w3id.org/mixs/vocab/subspecf_gen_lin) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | subspecific genetic lineage | +| **Comments:** | | Expected value: genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype | +| | | Position: 14.0 | +| **Examples:** | | Example(value='serovar:Newport', description=None) | + diff --git a/mixs6/substructure_type.md b/mixs6/substructure_type.md new file mode 100644 index 00000000..14d5432a --- /dev/null +++ b/mixs6/substructure_type.md @@ -0,0 +1,47 @@ + +# Slot: substructure_type + + +The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + +URI: [mixs.vocab:substructure_type](https://w3id.org/mixs/vocab/substructure_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | substructure type | +| **Mappings:** | | MIXS:0000767 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 19.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='basement', description=None) | + diff --git a/mixs6/sulfate.md b/mixs6/sulfate.md new file mode 100644 index 00000000..be49d46c --- /dev/null +++ b/mixs6/sulfate.md @@ -0,0 +1,108 @@ + +# Slot: sulfate + + +Concentration of sulfate in the sample + +URI: [mixs.vocab:sulfate](https://w3id.org/mixs/vocab/sulfate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sulfate | +| **Mappings:** | | MIXS:0000423 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 58.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5 micromole per liter', description=None) | + diff --git a/mixs6/sulfate_fw.md b/mixs6/sulfate_fw.md new file mode 100644 index 00000000..e8f152e5 --- /dev/null +++ b/mixs6/sulfate_fw.md @@ -0,0 +1,60 @@ + +# Slot: sulfate_fw + + +Original sulfate concentration in the hydrocarbon resource + +URI: [mixs.vocab:sulfate_fw](https://w3id.org/mixs/vocab/sulfate_fw) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sulfate in formation water | +| **Mappings:** | | MIXS:0000407 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 17.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sulfide.md b/mixs6/sulfide.md new file mode 100644 index 00000000..1fe3b74f --- /dev/null +++ b/mixs6/sulfide.md @@ -0,0 +1,108 @@ + +# Slot: sulfide + + +Concentration of sulfide in the sample + +URI: [mixs.vocab:sulfide](https://w3id.org/mixs/vocab/sulfide) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sulfide | +| **Mappings:** | | MIXS:0000424 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 59.0 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='2 micromole per liter', description=None) | + diff --git a/mixs6/surf_air_cont.md b/mixs6/surf_air_cont.md new file mode 100644 index 00000000..c0108d93 --- /dev/null +++ b/mixs6/surf_air_cont.md @@ -0,0 +1,47 @@ + +# Slot: surf_air_cont + + +Contaminant identified on surface + +URI: [mixs.vocab:surf_air_cont](https://w3id.org/mixs/vocab/surf_air_cont) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface-air contaminant | +| **Mappings:** | | MIXS:0000759 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 2.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='radon', description=None) | + diff --git a/mixs6/surf_humidity.md b/mixs6/surf_humidity.md new file mode 100644 index 00000000..9ba9e579 --- /dev/null +++ b/mixs6/surf_humidity.md @@ -0,0 +1,48 @@ + +# Slot: surf_humidity + + +Surfaces: water activity as a function of air and material moisture + +URI: [mixs.vocab:surf_humidity](https://w3id.org/mixs/vocab/surf_humidity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface humidity | +| **Mappings:** | | MIXS:0000123 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 5.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='10%', description=None) | + diff --git a/mixs6/surf_material.md b/mixs6/surf_material.md new file mode 100644 index 00000000..2b6cf9b9 --- /dev/null +++ b/mixs6/surf_material.md @@ -0,0 +1,47 @@ + +# Slot: surf_material + + +Surface materials at the point of sampling + +URI: [mixs.vocab:surf_material](https://w3id.org/mixs/vocab/surf_material) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface material | +| **Mappings:** | | MIXS:0000758 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/surf_moisture.md b/mixs6/surf_moisture.md new file mode 100644 index 00000000..bb1aa5b6 --- /dev/null +++ b/mixs6/surf_moisture.md @@ -0,0 +1,48 @@ + +# Slot: surf_moisture + + +Water held on a surface + +URI: [mixs.vocab:surf_moisture](https://w3id.org/mixs/vocab/surf_moisture) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface moisture | +| **Mappings:** | | MIXS:0000128 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: parts per million, gram per cubic meter, gram per square meter | +| | | Occurrence: 1 | +| | | Position: 10.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='0.01 gram per square meter', description=None) | + diff --git a/mixs6/surf_moisture_ph.md b/mixs6/surf_moisture_ph.md new file mode 100644 index 00000000..338cb57c --- /dev/null +++ b/mixs6/surf_moisture_ph.md @@ -0,0 +1,47 @@ + +# Slot: surf_moisture_ph + + +ph measurement of surface + +URI: [mixs.vocab:surf_moisture_ph](https://w3id.org/mixs/vocab/surf_moisture_ph) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface moisture pH | +| **Mappings:** | | MIXS:0000760 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 8.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='7', description=None) | + diff --git a/mixs6/surf_temp.md b/mixs6/surf_temp.md new file mode 100644 index 00000000..96707552 --- /dev/null +++ b/mixs6/surf_temp.md @@ -0,0 +1,48 @@ + +# Slot: surf_temp + + +Temperature of the surface at the time of sampling + +URI: [mixs.vocab:surf_temp](https://w3id.org/mixs/vocab/surf_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface temperature | +| **Mappings:** | | MIXS:0000125 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 7.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='15 degree Celsius', description=None) | + diff --git a/mixs6/suspend_part_matter.md b/mixs6/suspend_part_matter.md new file mode 100644 index 00000000..a9acd74f --- /dev/null +++ b/mixs6/suspend_part_matter.md @@ -0,0 +1,48 @@ + +# Slot: suspend_part_matter + + +Concentration of suspended particulate matter + +URI: [mixs.vocab:suspend_part_matter](https://w3id.org/mixs/vocab/suspend_part_matter) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | suspended particulate matter | +| **Mappings:** | | MIXS:0000741 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.5 milligram per liter', description=None) | + diff --git a/mixs6/suspend_solids.md b/mixs6/suspend_solids.md new file mode 100644 index 00000000..002b4cee --- /dev/null +++ b/mixs6/suspend_solids.md @@ -0,0 +1,72 @@ + +# Slot: suspend_solids + + +Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + +URI: [mixs.vocab:suspend_solids](https://w3id.org/mixs/vocab/suspend_solids) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | suspended solids | +| **Mappings:** | | MIXS:0000150 | +| **Comments:** | | Expected value: suspended solid name;measurement value | +| | | Preferred unit: gram, microgram, milligram per liter, mole per liter, gram per liter, part per million | +| | | Occurrence: m | +| | | Position: 76.0 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tan.md b/mixs6/tan.md new file mode 100644 index 00000000..70559516 --- /dev/null +++ b/mixs6/tan.md @@ -0,0 +1,60 @@ + +# Slot: tan + + +Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + +URI: [mixs.vocab:tan](https://w3id.org/mixs/vocab/tan) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total acid number | +| **Mappings:** | | MIXS:0000120 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 86.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/target_gene.md b/mixs6/target_gene.md new file mode 100644 index 00000000..11c10f64 --- /dev/null +++ b/mixs6/target_gene.md @@ -0,0 +1,35 @@ + +# Slot: target_gene + + +Targeted gene or locus name for marker gene studies + +URI: [mixs.vocab:target_gene](https://w3id.org/mixs/vocab/target_gene) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | target gene | +| **Comments:** | | Expected value: gene name | +| | | Position: 44.0 | +| **Examples:** | | Example(value='16S rRNA, 18S rRNA, nif, amoA, rpo', description=None) | + diff --git a/mixs6/target_subfragment.md b/mixs6/target_subfragment.md new file mode 100644 index 00000000..79870f66 --- /dev/null +++ b/mixs6/target_subfragment.md @@ -0,0 +1,35 @@ + +# Slot: target_subfragment + + +Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + +URI: [mixs.vocab:target_subfragment](https://w3id.org/mixs/vocab/target_subfragment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | target subfragment | +| **Comments:** | | Expected value: gene fragment name | +| | | Position: 45.0 | +| **Examples:** | | Example(value='V6, V9, ITS', description=None) | + diff --git a/mixs6/tax_class.md b/mixs6/tax_class.md new file mode 100644 index 00000000..551f7374 --- /dev/null +++ b/mixs6/tax_class.md @@ -0,0 +1,42 @@ + +# Slot: tax_class + + +Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + +URI: [mixs.vocab:tax_class](https://w3id.org/mixs/vocab/tax_class) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞tax_class](ME_tax_class.md) + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) + * [MIGS org➞tax_class](MIGS_org_tax_class.md) + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) + * [MIMAG➞tax_class](MIMAG_tax_class.md) + * [MISAG➞tax_class](MISAG_tax_class.md) + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | taxonomic classification | +| **Comments:** | | Expected value: classification method, database name, and other parameters | +| | | Position: 62.0 | +| **Examples:** | | Example(value='vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)', description=None) | + diff --git a/mixs6/tax_ident.md b/mixs6/tax_ident.md new file mode 100644 index 00000000..68c73e14 --- /dev/null +++ b/mixs6/tax_ident.md @@ -0,0 +1,41 @@ + +# Slot: tax_ident + + +The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + +URI: [mixs.vocab:tax_ident](https://w3id.org/mixs/vocab/tax_ident) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) + * [MISAG➞tax_ident](MISAG_tax_ident.md) + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | taxonomic identity marker | +| **Comments:** | | Expected value: enumeration | +| | | Position: 53.0 | +| **Examples:** | | Example(value='other: rpoB gene', description=None) | + diff --git a/mixs6/temp.md b/mixs6/temp.md new file mode 100644 index 00000000..062bda66 --- /dev/null +++ b/mixs6/temp.md @@ -0,0 +1,216 @@ + +# Slot: temp + + +Temperature of the sample at the time of sampling + +URI: [mixs.vocab:temp](https://w3id.org/mixs/vocab/temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | temperature | +| **Mappings:** | | MIXS:0000113 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='25 degree Celsius', description=None) | + diff --git a/mixs6/temp_out.md b/mixs6/temp_out.md new file mode 100644 index 00000000..a76b78f6 --- /dev/null +++ b/mixs6/temp_out.md @@ -0,0 +1,48 @@ + +# Slot: temp_out + + +The recorded temperature value at sampling time outside + +URI: [mixs.vocab:temp_out](https://w3id.org/mixs/vocab/temp_out) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | temperature outside house | +| **Mappings:** | | MIXS:0000197 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 133.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='5 degree Celsius', description=None) | + diff --git a/mixs6/tertiary_treatment.md b/mixs6/tertiary_treatment.md new file mode 100644 index 00000000..5803022c --- /dev/null +++ b/mixs6/tertiary_treatment.md @@ -0,0 +1,47 @@ + +# Slot: tertiary_treatment + + +The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + +URI: [mixs.vocab:tertiary_treatment](https://w3id.org/mixs/vocab/tertiary_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tertiary treatment | +| **Mappings:** | | MIXS:0000352 | +| **Comments:** | | Expected value: tertiary treatment type | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/texture.md b/mixs6/texture.md new file mode 100644 index 00000000..afc767e8 --- /dev/null +++ b/mixs6/texture.md @@ -0,0 +1,47 @@ + +# Slot: texture + + +The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + +URI: [mixs.vocab:texture](https://w3id.org/mixs/vocab/texture) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | texture | +| **Mappings:** | | MIXS:0000335 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 35.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/texture_meth.md b/mixs6/texture_meth.md new file mode 100644 index 00000000..f741d2e0 --- /dev/null +++ b/mixs6/texture_meth.md @@ -0,0 +1,47 @@ + +# Slot: texture_meth + + +Reference or method used in determining soil texture + +URI: [mixs.vocab:texture_meth](https://w3id.org/mixs/vocab/texture_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | texture method | +| **Mappings:** | | MIXS:0000336 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 36.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tidal_stage.md b/mixs6/tidal_stage.md new file mode 100644 index 00000000..dd33cb20 --- /dev/null +++ b/mixs6/tidal_stage.md @@ -0,0 +1,59 @@ + +# Slot: tidal_stage + + +Stage of tide + +URI: [mixs.vocab:tidal_stage](https://w3id.org/mixs/vocab/tidal_stage) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tidal stage | +| **Mappings:** | | MIXS:0000750 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: sediment, water | +| **Examples:** | | Example(value='high tide', description=None) | + diff --git a/mixs6/tillage.md b/mixs6/tillage.md new file mode 100644 index 00000000..ae63e81d --- /dev/null +++ b/mixs6/tillage.md @@ -0,0 +1,47 @@ + +# Slot: tillage + + +Note method(s) used for tilling + +URI: [mixs.vocab:tillage](https://w3id.org/mixs/vocab/tillage) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/tillage | +| **Mappings:** | | MIXS:0001081 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: m | +| | | Position: 8.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='chisel', description=None) | + diff --git a/mixs6/time_last_toothbrush.md b/mixs6/time_last_toothbrush.md new file mode 100644 index 00000000..7fa8a55f --- /dev/null +++ b/mixs6/time_last_toothbrush.md @@ -0,0 +1,47 @@ + +# Slot: time_last_toothbrush + + +Specification of the time since last toothbrushing + +URI: [mixs.vocab:time_last_toothbrush](https://w3id.org/mixs/vocab/time_last_toothbrush) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | time since last toothbrushing | +| **Mappings:** | | MIXS:0000924 | +| **Comments:** | | Expected value: duration | +| | | Occurrence: 1 | +| | | Position: 2.0 | +| | | This field is used uniquely in: human-oral | +| **Examples:** | | Example(value='P2H45M', description=None) | + diff --git a/mixs6/time_since_last_wash.md b/mixs6/time_since_last_wash.md new file mode 100644 index 00000000..b37b4117 --- /dev/null +++ b/mixs6/time_since_last_wash.md @@ -0,0 +1,47 @@ + +# Slot: time_since_last_wash + + +Specification of the time since last wash + +URI: [mixs.vocab:time_since_last_wash](https://w3id.org/mixs/vocab/time_since_last_wash) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | time since last wash | +| **Mappings:** | | MIXS:0000943 | +| **Comments:** | | Expected value: duration | +| | | Occurrence: 1 | +| | | Position: 2.0 | +| | | This field is used uniquely in: human-skin | +| **Examples:** | | Example(value='P1D', description=None) | + diff --git a/mixs6/tiss_cult_growth_med.md b/mixs6/tiss_cult_growth_med.md new file mode 100644 index 00000000..16000de1 --- /dev/null +++ b/mixs6/tiss_cult_growth_med.md @@ -0,0 +1,47 @@ + +# Slot: tiss_cult_growth_med + + +Description of plant tissue culture growth media used + +URI: [mixs.vocab:tiss_cult_growth_med](https://w3id.org/mixs/vocab/tiss_cult_growth_med) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tissue culture growth media | +| **Mappings:** | | MIXS:0001070 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='https://link.springer.com/content/pdf/10.1007/BF02796489.pdf', description=None) | + diff --git a/mixs6/toluene.md b/mixs6/toluene.md new file mode 100644 index 00000000..726de363 --- /dev/null +++ b/mixs6/toluene.md @@ -0,0 +1,60 @@ + +# Slot: toluene + + +Concentration of toluene in the sample + +URI: [mixs.vocab:toluene](https://w3id.org/mixs/vocab/toluene) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | toluene | +| **Mappings:** | | MIXS:0000154 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 82.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_carb.md b/mixs6/tot_carb.md new file mode 100644 index 00000000..623233b5 --- /dev/null +++ b/mixs6/tot_carb.md @@ -0,0 +1,60 @@ + +# Slot: tot_carb + + +Total carbon content + +URI: [mixs.vocab:tot_carb](https://w3id.org/mixs/vocab/tot_carb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total carbon | +| **Mappings:** | | MIXS:0000525 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: microbial mat_biofilm, sediment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_depth_water_col.md b/mixs6/tot_depth_water_col.md new file mode 100644 index 00000000..d720b0de --- /dev/null +++ b/mixs6/tot_depth_water_col.md @@ -0,0 +1,60 @@ + +# Slot: tot_depth_water_col + + +Measurement of total depth of water column + +URI: [mixs.vocab:tot_depth_water_col](https://w3id.org/mixs/vocab/tot_depth_water_col) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total depth of water column | +| **Mappings:** | | MIXS:0000634 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: sediment, water | +| **Examples:** | | Example(value='500 meter', description=None) | + diff --git a/mixs6/tot_diss_nitro.md b/mixs6/tot_diss_nitro.md new file mode 100644 index 00000000..1026b816 --- /dev/null +++ b/mixs6/tot_diss_nitro.md @@ -0,0 +1,48 @@ + +# Slot: tot_diss_nitro + + +Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + +URI: [mixs.vocab:tot_diss_nitro](https://w3id.org/mixs/vocab/tot_diss_nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total dissolved nitrogen | +| **Mappings:** | | MIXS:0000744 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='40 microgram per liter', description=None) | + diff --git a/mixs6/tot_inorg_nitro.md b/mixs6/tot_inorg_nitro.md new file mode 100644 index 00000000..829ff123 --- /dev/null +++ b/mixs6/tot_inorg_nitro.md @@ -0,0 +1,48 @@ + +# Slot: tot_inorg_nitro + + +Total inorganic nitrogen content + +URI: [mixs.vocab:tot_inorg_nitro](https://w3id.org/mixs/vocab/tot_inorg_nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total inorganic nitrogen | +| **Mappings:** | | MIXS:0000745 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='40 microgram per liter', description=None) | + diff --git a/mixs6/tot_iron.md b/mixs6/tot_iron.md new file mode 100644 index 00000000..1ef01b7c --- /dev/null +++ b/mixs6/tot_iron.md @@ -0,0 +1,60 @@ + +# Slot: tot_iron + + +Concentration of total iron in the sample + +URI: [mixs.vocab:tot_iron](https://w3id.org/mixs/vocab/tot_iron) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total iron | +| **Mappings:** | | MIXS:0000105 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, milligram per kilogram | +| | | Occurrence: 1 | +| | | Position: 71.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_nitro.md b/mixs6/tot_nitro.md new file mode 100644 index 00000000..0a4d244e --- /dev/null +++ b/mixs6/tot_nitro.md @@ -0,0 +1,84 @@ + +# Slot: tot_nitro + + +Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + +URI: [mixs.vocab:tot_nitro](https://w3id.org/mixs/vocab/tot_nitro) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total nitrogen concentration | +| **Mappings:** | | MIXS:0000102 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 64.0 | +| | | This field is used in: 4 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, wastewater_sludge, water | +| **Examples:** | | Example(value='50 micromole per liter', description=None) | + diff --git a/mixs6/tot_nitro_content.md b/mixs6/tot_nitro_content.md new file mode 100644 index 00000000..28610c03 --- /dev/null +++ b/mixs6/tot_nitro_content.md @@ -0,0 +1,72 @@ + +# Slot: tot_nitro_content + + +Total nitrogen content of the sample + +URI: [mixs.vocab:tot_nitro_content](https://w3id.org/mixs/vocab/tot_nitro_content) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total nitrogen content | +| **Mappings:** | | MIXS:0000530 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_nitro_content_meth.md b/mixs6/tot_nitro_content_meth.md new file mode 100644 index 00000000..faa38921 --- /dev/null +++ b/mixs6/tot_nitro_content_meth.md @@ -0,0 +1,47 @@ + +# Slot: tot_nitro_content_meth + + +Reference or method used in determining the total nitrogen + +URI: [mixs.vocab:tot_nitro_content_meth](https://w3id.org/mixs/vocab/tot_nitro_content_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total nitrogen content method | +| **Mappings:** | | MIXS:0000338 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 42.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_org_c_meth.md b/mixs6/tot_org_c_meth.md new file mode 100644 index 00000000..152d1ab1 --- /dev/null +++ b/mixs6/tot_org_c_meth.md @@ -0,0 +1,47 @@ + +# Slot: tot_org_c_meth + + +Reference or method used in determining total organic carbon + +URI: [mixs.vocab:tot_org_c_meth](https://w3id.org/mixs/vocab/tot_org_c_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total organic carbon method | +| **Mappings:** | | MIXS:0000337 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 40.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_org_carb.md b/mixs6/tot_org_carb.md new file mode 100644 index 00000000..7d36f2dc --- /dev/null +++ b/mixs6/tot_org_carb.md @@ -0,0 +1,72 @@ + +# Slot: tot_org_carb + + +Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + +URI: [mixs.vocab:tot_org_carb](https://w3id.org/mixs/vocab/tot_org_carb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total organic carbon | +| **Mappings:** | | MIXS:0000533 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram Carbon per kilogram sample material | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_part_carb.md b/mixs6/tot_part_carb.md new file mode 100644 index 00000000..1cbf6232 --- /dev/null +++ b/mixs6/tot_part_carb.md @@ -0,0 +1,48 @@ + +# Slot: tot_part_carb + + +Total particulate carbon content + +URI: [mixs.vocab:tot_part_carb](https://w3id.org/mixs/vocab/tot_part_carb) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total particulate carbon | +| **Mappings:** | | MIXS:0000747 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='35 micromole per liter', description=None) | + diff --git a/mixs6/tot_phosp.md b/mixs6/tot_phosp.md new file mode 100644 index 00000000..559784c5 --- /dev/null +++ b/mixs6/tot_phosp.md @@ -0,0 +1,72 @@ + +# Slot: tot_phosp + + +Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + +URI: [mixs.vocab:tot_phosp](https://w3id.org/mixs/vocab/tot_phosp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total phosphorus | +| **Mappings:** | | MIXS:0000117 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 75.0 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | +| **Examples:** | | Example(value='0.03 milligram per liter', description=None) | + diff --git a/mixs6/tot_phosphate.md b/mixs6/tot_phosphate.md new file mode 100644 index 00000000..ea1dcdbd --- /dev/null +++ b/mixs6/tot_phosphate.md @@ -0,0 +1,48 @@ + +# Slot: tot_phosphate + + +Total amount or concentration of phosphate + +URI: [mixs.vocab:tot_phosphate](https://w3id.org/mixs/vocab/tot_phosphate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total phosphate | +| **Mappings:** | | MIXS:0000689 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_sulfur.md b/mixs6/tot_sulfur.md new file mode 100644 index 00000000..2f31fd1d --- /dev/null +++ b/mixs6/tot_sulfur.md @@ -0,0 +1,60 @@ + +# Slot: tot_sulfur + + +Concentration of total sulfur in the sample + +URI: [mixs.vocab:tot_sulfur](https://w3id.org/mixs/vocab/tot_sulfur) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total sulfur | +| **Mappings:** | | MIXS:0000419 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 60.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/train_line.md b/mixs6/train_line.md new file mode 100644 index 00000000..a37c038e --- /dev/null +++ b/mixs6/train_line.md @@ -0,0 +1,47 @@ + +# Slot: train_line + + +The subway line name + +URI: [mixs.vocab:train_line](https://w3id.org/mixs/vocab/train_line) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | train line | +| **Mappings:** | | MIXS:0000837 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 134.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='red', description=None) | + diff --git a/mixs6/train_stat_loc.md b/mixs6/train_stat_loc.md new file mode 100644 index 00000000..e15e09c8 --- /dev/null +++ b/mixs6/train_stat_loc.md @@ -0,0 +1,47 @@ + +# Slot: train_stat_loc + + +The train station collection location + +URI: [mixs.vocab:train_stat_loc](https://w3id.org/mixs/vocab/train_stat_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | train station collection location | +| **Mappings:** | | MIXS:0000838 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 135.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='forest hills', description=None) | + diff --git a/mixs6/train_stop_loc.md b/mixs6/train_stop_loc.md new file mode 100644 index 00000000..f6ffbceb --- /dev/null +++ b/mixs6/train_stop_loc.md @@ -0,0 +1,47 @@ + +# Slot: train_stop_loc + + +The train stop collection location + +URI: [mixs.vocab:train_stop_loc](https://w3id.org/mixs/vocab/train_stop_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | train stop collection location | +| **Mappings:** | | MIXS:0000839 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 136.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='end', description=None) | + diff --git a/mixs6/travel_out_six_month.md b/mixs6/travel_out_six_month.md new file mode 100644 index 00000000..7371391e --- /dev/null +++ b/mixs6/travel_out_six_month.md @@ -0,0 +1,47 @@ + +# Slot: travel_out_six_month + + +Specification of the countries travelled in the last six months; can include multiple travels + +URI: [mixs.vocab:travel_out_six_month](https://w3id.org/mixs/vocab/travel_out_six_month) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | travel outside the country in last six months | +| **Mappings:** | | MIXS:0000268 | +| **Comments:** | | Expected value: country name | +| | | Occurrence: m | +| | | Position: 26.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/trna_ext_software.md b/mixs6/trna_ext_software.md new file mode 100644 index 00000000..47678922 --- /dev/null +++ b/mixs6/trna_ext_software.md @@ -0,0 +1,36 @@ + +# Slot: trna_ext_software + + +Tools used for tRNA identification + +URI: [mixs.vocab:trna_ext_software](https://w3id.org/mixs/vocab/trna_ext_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tRNA extraction software | +| **Comments:** | | Expected value: names and versions of software(s), parameters used | +| | | Position: 66.0 | +| **Examples:** | | Example(value='infernal;v2;default parameters', description=None) | + diff --git a/mixs6/trnas.md b/mixs6/trnas.md new file mode 100644 index 00000000..4fcce512 --- /dev/null +++ b/mixs6/trnas.md @@ -0,0 +1,36 @@ + +# Slot: trnas + + +The total number of tRNAs identified from the SAG or MAG + +URI: [mixs.vocab:trnas](https://w3id.org/mixs/vocab/trnas) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞trnas](MIMAG_trnas.md) + * [MISAG➞trnas](MISAG_trnas.md) + * [MIUVIG➞trnas](MIUVIG_trnas.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of standard tRNAs extracted | +| **Comments:** | | Expected value: value from 0-21 | +| | | Position: 65.0 | +| **Examples:** | | Example(value='18', description=None) | + diff --git a/mixs6/trophic_level.md b/mixs6/trophic_level.md new file mode 100644 index 00000000..e3f0d2a2 --- /dev/null +++ b/mixs6/trophic_level.md @@ -0,0 +1,36 @@ + +# Slot: trophic_level + + +Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + +URI: [mixs.vocab:trophic_level](https://w3id.org/mixs/vocab/trophic_level) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | trophic level | +| **Comments:** | | Expected value: enumeration | +| | | Position: 26.0 | +| **Examples:** | | Example(value='heterotroph', description=None) | + diff --git a/mixs6/turbidity.md b/mixs6/turbidity.md new file mode 100644 index 00000000..dd7ad58e --- /dev/null +++ b/mixs6/turbidity.md @@ -0,0 +1,72 @@ + +# Slot: turbidity + + +Measure of the amount of cloudiness or haziness in water caused by individual particles + +URI: [mixs.vocab:turbidity](https://w3id.org/mixs/vocab/turbidity) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | turbidity | +| **Mappings:** | | MIXS:0000191 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: formazin turbidity unit, formazin nephelometric units | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.3 nephelometric turbidity units', description=None) | + diff --git a/mixs6/tvdss_of_hcr_pressure.md b/mixs6/tvdss_of_hcr_pressure.md new file mode 100644 index 00000000..fc9558ce --- /dev/null +++ b/mixs6/tvdss_of_hcr_pressure.md @@ -0,0 +1,60 @@ + +# Slot: tvdss_of_hcr_pressure + + +True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + +URI: [mixs.vocab:tvdss_of_hcr_pressure](https://w3id.org/mixs/vocab/tvdss_of_hcr_pressure) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | depth (TVDSS) of hydrocarbon resource pressure | +| **Mappings:** | | MIXS:0000397 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 9.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tvdss_of_hcr_temp.md b/mixs6/tvdss_of_hcr_temp.md new file mode 100644 index 00000000..b7e281a5 --- /dev/null +++ b/mixs6/tvdss_of_hcr_temp.md @@ -0,0 +1,60 @@ + +# Slot: tvdss_of_hcr_temp + + +True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + +URI: [mixs.vocab:tvdss_of_hcr_temp](https://w3id.org/mixs/vocab/tvdss_of_hcr_temp) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | depth (TVDSS) of hydrocarbon resource temperature | +| **Mappings:** | | MIXS:0000394 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 7.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/twin_sibling.md b/mixs6/twin_sibling.md new file mode 100644 index 00000000..0c37d3a4 --- /dev/null +++ b/mixs6/twin_sibling.md @@ -0,0 +1,47 @@ + +# Slot: twin_sibling + + +Specification of twin sibling presence + +URI: [mixs.vocab:twin_sibling](https://w3id.org/mixs/vocab/twin_sibling) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | twin sibling presence | +| **Mappings:** | | MIXS:0000326 | +| **Comments:** | | Expected value: presence status | +| | | Occurrence: 1 | +| | | Position: 27.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/typ_occup_density.md b/mixs6/typ_occup_density.md new file mode 100644 index 00000000..80f8991b --- /dev/null +++ b/mixs6/typ_occup_density.md @@ -0,0 +1,47 @@ + +# Slot: typ_occup_density + + +Customary or normal density of occupants + +URI: [mixs.vocab:typ_occup_density](https://w3id.org/mixs/vocab/typ_occup_density) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | typical occupant density | +| **Mappings:** | | MIXS:0000771 | +| **Comments:** | | Expected value: measurement value | +| | | Occurrence: 1 | +| | | Position: 24.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='25', description=None) | + diff --git a/mixs6/urine_collect_meth.md b/mixs6/urine_collect_meth.md new file mode 100644 index 00000000..fff2520f --- /dev/null +++ b/mixs6/urine_collect_meth.md @@ -0,0 +1,47 @@ + +# Slot: urine_collect_meth + + +Specification of urine collection method + +URI: [mixs.vocab:urine_collect_meth](https://w3id.org/mixs/vocab/urine_collect_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urine/collection method | +| **Mappings:** | | MIXS:0000899 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 43.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='catheter', description=None) | + diff --git a/mixs6/url.md b/mixs6/url.md new file mode 100644 index 00000000..fd52ae53 --- /dev/null +++ b/mixs6/url.md @@ -0,0 +1,45 @@ + +# Slot: url + + + + +URI: [mixs.vocab:url](https://w3id.org/mixs/vocab/url) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [ME➞url](ME_url.md) + * [MIGS bacteria➞url](MIGS_bacteria_url.md) + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) + * [MIGS org➞url](MIGS_org_url.md) + * [MIGS plant➞url](MIGS_plant_url.md) + * [MIGS virus➞url](MIGS_virus_url.md) + * [MIMAG➞url](MIMAG_url.md) + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) + * [MIMARKS survey➞url](MIMARKS_survey_url.md) + * [MISAG➞url](MISAG_url.md) + * [MIUVIG➞url](MIUVIG_url.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relevant electronic resources | +| **Comments:** | | Expected value: URL | +| | | Position: 92.0 | +| **Examples:** | | Example(value='http://www.earthmicrobiome.org/', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/67 | + diff --git a/mixs6/urogenit_disord.md b/mixs6/urogenit_disord.md new file mode 100644 index 00000000..0b02efad --- /dev/null +++ b/mixs6/urogenit_disord.md @@ -0,0 +1,47 @@ + +# Slot: urogenit_disord + + +History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + +URI: [mixs.vocab:urogenit_disord](https://w3id.org/mixs/vocab/urogenit_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urogenital disorder | +| **Mappings:** | | MIXS:0000289 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 10.0 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/urogenit_tract_disor.md b/mixs6/urogenit_tract_disor.md new file mode 100644 index 00000000..1c7f6693 --- /dev/null +++ b/mixs6/urogenit_tract_disor.md @@ -0,0 +1,47 @@ + +# Slot: urogenit_tract_disor + + +History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + +URI: [mixs.vocab:urogenit_tract_disor](https://w3id.org/mixs/vocab/urogenit_tract_disor) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urine/urogenital tract disorder | +| **Mappings:** | | MIXS:0000278 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 41.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ventilation_rate.md b/mixs6/ventilation_rate.md new file mode 100644 index 00000000..29e58a7f --- /dev/null +++ b/mixs6/ventilation_rate.md @@ -0,0 +1,48 @@ + +# Slot: ventilation_rate + + +Ventilation rate of the system in the sampled premises + +URI: [mixs.vocab:ventilation_rate](https://w3id.org/mixs/vocab/ventilation_rate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ventilation rate | +| **Mappings:** | | MIXS:0000114 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per minute, liters per second | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='750 cubic meter per minute', description=None) | + diff --git a/mixs6/ventilation_type.md b/mixs6/ventilation_type.md new file mode 100644 index 00000000..049fb7e3 --- /dev/null +++ b/mixs6/ventilation_type.md @@ -0,0 +1,59 @@ + +# Slot: ventilation_type + + +Ventilation system used in the sampled premises + +URI: [mixs.vocab:ventilation_type](https://w3id.org/mixs/vocab/ventilation_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ventilation type | +| **Mappings:** | | MIXS:0000756 | +| **Comments:** | | Expected value: ventilation type name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: air, built environment | +| **Examples:** | | Example(value='Operable windows', description=None) | + diff --git a/mixs6/vfa.md b/mixs6/vfa.md new file mode 100644 index 00000000..48395a33 --- /dev/null +++ b/mixs6/vfa.md @@ -0,0 +1,60 @@ + +# Slot: vfa + + +Concentration of Volatile Fatty Acids in the sample + +URI: [mixs.vocab:vfa](https://w3id.org/mixs/vocab/vfa) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | volatile fatty acids | +| **Mappings:** | | MIXS:0000152 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 80.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/vfa_fw.md b/mixs6/vfa_fw.md new file mode 100644 index 00000000..6f235c99 --- /dev/null +++ b/mixs6/vfa_fw.md @@ -0,0 +1,60 @@ + +# Slot: vfa_fw + + +Original volatile fatty acid concentration in the hydrocarbon resource + +URI: [mixs.vocab:vfa_fw](https://w3id.org/mixs/vocab/vfa_fw) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vfa in formation water | +| **Mappings:** | | MIXS:0000408 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 18.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/vir_ident_software.md b/mixs6/vir_ident_software.md new file mode 100644 index 00000000..0319feee --- /dev/null +++ b/mixs6/vir_ident_software.md @@ -0,0 +1,34 @@ + +# Slot: vir_ident_software + + +Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + +URI: [mixs.vocab:vir_ident_software](https://w3id.org/mixs/vocab/vir_ident_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | viral identification software | +| **Comments:** | | Expected value: software name, version and relevant parameters | +| | | Position: 83.0 | +| **Examples:** | | Example(value='VirSorter; 1.0.4; Virome database, category 2', description=None) | + diff --git a/mixs6/virus_enrich_appr.md b/mixs6/virus_enrich_appr.md new file mode 100644 index 00000000..4fcccf6f --- /dev/null +++ b/mixs6/virus_enrich_appr.md @@ -0,0 +1,35 @@ + +# Slot: virus_enrich_appr + + +List of approaches used to enrich the sample for viruses, if any + +URI: [mixs.vocab:virus_enrich_appr](https://w3id.org/mixs/vocab/virus_enrich_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | virus enrichment approach | +| **Comments:** | | Expected value: enumeration | +| | | Position: 36.0 | +| **Examples:** | | Example(value='filtration + FeCl Precipitation + ultracentrifugation + DNAse', description=None) | + diff --git a/mixs6/vis_media.md b/mixs6/vis_media.md new file mode 100644 index 00000000..e59beaf3 --- /dev/null +++ b/mixs6/vis_media.md @@ -0,0 +1,47 @@ + +# Slot: vis_media + + +The building visual media + +URI: [mixs.vocab:vis_media](https://w3id.org/mixs/vocab/vis_media) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | visual media | +| **Mappings:** | | MIXS:0000840 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 137.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='3D scans', description=None) | + diff --git a/mixs6/viscosity.md b/mixs6/viscosity.md new file mode 100644 index 00000000..934f78bf --- /dev/null +++ b/mixs6/viscosity.md @@ -0,0 +1,60 @@ + +# Slot: viscosity + + +A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + +URI: [mixs.vocab:viscosity](https://w3id.org/mixs/vocab/viscosity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | viscosity | +| **Mappings:** | | MIXS:0000126 | +| **Comments:** | | Expected value: measurement value;measurement value | +| | | Preferred unit: cP at degree Celsius | +| | | Occurrence: 1 | +| | | Position: 87.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/volatile_org_comp.md b/mixs6/volatile_org_comp.md new file mode 100644 index 00000000..85198752 --- /dev/null +++ b/mixs6/volatile_org_comp.md @@ -0,0 +1,48 @@ + +# Slot: volatile_org_comp + + +Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + +URI: [mixs.vocab:volatile_org_comp](https://w3id.org/mixs/vocab/volatile_org_comp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | volatile organic compounds | +| **Mappings:** | | MIXS:0000115 | +| **Comments:** | | Expected value: volatile organic compound name;measurement value | +| | | Preferred unit: microgram per cubic meter, parts per million, nanogram per liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='formaldehyde;500 nanogram per liter', description=None) | + diff --git a/mixs6/votu_class_appr.md b/mixs6/votu_class_appr.md new file mode 100644 index 00000000..86008679 --- /dev/null +++ b/mixs6/votu_class_appr.md @@ -0,0 +1,34 @@ + +# Slot: votu_class_appr + + +Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + +URI: [mixs.vocab:votu_class_appr](https://w3id.org/mixs/vocab/votu_class_appr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vOTU classification approach | +| **Comments:** | | Expected value: cutoffs and method used | +| | | Position: 87.0 | +| **Examples:** | | Example(value='95% ANI;85% AF; greedy incremental clustering', description=None) | + diff --git a/mixs6/votu_db.md b/mixs6/votu_db.md new file mode 100644 index 00000000..256cbe4b --- /dev/null +++ b/mixs6/votu_db.md @@ -0,0 +1,34 @@ + +# Slot: votu_db + + +Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + +URI: [mixs.vocab:votu_db](https://w3id.org/mixs/vocab/votu_db) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vOTU database | +| **Comments:** | | Expected value: database and version | +| | | Position: 89.0 | +| **Examples:** | | Example(value='NCBI Viral RefSeq;83', description=None) | + diff --git a/mixs6/votu_seq_comp_appr.md b/mixs6/votu_seq_comp_appr.md new file mode 100644 index 00000000..94d749c0 --- /dev/null +++ b/mixs6/votu_seq_comp_appr.md @@ -0,0 +1,34 @@ + +# Slot: votu_seq_comp_appr + + +Tool and thresholds used to compare sequences when computing "species-level" vOTUs + +URI: [mixs.vocab:votu_seq_comp_appr](https://w3id.org/mixs/vocab/votu_seq_comp_appr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vOTU sequence comparison approach | +| **Comments:** | | Expected value: software name, version and relevant parameters | +| | | Position: 88.0 | +| **Examples:** | | Example(value='blastn;2.6.0+;e-value cutoff: 0.001', description=None) | + diff --git a/mixs6/wall_area.md b/mixs6/wall_area.md new file mode 100644 index 00000000..772e032c --- /dev/null +++ b/mixs6/wall_area.md @@ -0,0 +1,48 @@ + +# Slot: wall_area + + +The total area of the sampled room's walls + +URI: [mixs.vocab:wall_area](https://w3id.org/mixs/vocab/wall_area) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall area | +| **Mappings:** | | MIXS:0000198 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 138.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wall_const_type.md b/mixs6/wall_const_type.md new file mode 100644 index 00000000..c71506fc --- /dev/null +++ b/mixs6/wall_const_type.md @@ -0,0 +1,47 @@ + +# Slot: wall_const_type + + +The building class of the wall defined by the composition of the building elements and fire-resistance rating. + +URI: [mixs.vocab:wall_const_type](https://w3id.org/mixs/vocab/wall_const_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall construction type | +| **Mappings:** | | MIXS:0000841 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 139.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='fire resistive', description=None) | + diff --git a/mixs6/wall_finish_mat.md b/mixs6/wall_finish_mat.md new file mode 100644 index 00000000..ee565ae8 --- /dev/null +++ b/mixs6/wall_finish_mat.md @@ -0,0 +1,47 @@ + +# Slot: wall_finish_mat + + +The material utilized to finish the outer most layer of the wall + +URI: [mixs.vocab:wall_finish_mat](https://w3id.org/mixs/vocab/wall_finish_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall finish material | +| **Mappings:** | | MIXS:0000842 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 140.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/wall_height.md b/mixs6/wall_height.md new file mode 100644 index 00000000..70b2e2b1 --- /dev/null +++ b/mixs6/wall_height.md @@ -0,0 +1,48 @@ + +# Slot: wall_height + + +The average height of the walls in the sampled room + +URI: [mixs.vocab:wall_height](https://w3id.org/mixs/vocab/wall_height) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall height | +| **Mappings:** | | MIXS:0000221 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: centimeter | +| | | Occurrence: 1 | +| | | Position: 141.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wall_loc.md b/mixs6/wall_loc.md new file mode 100644 index 00000000..9e377510 --- /dev/null +++ b/mixs6/wall_loc.md @@ -0,0 +1,47 @@ + +# Slot: wall_loc + + +The relative location of the wall within the room + +URI: [mixs.vocab:wall_loc](https://w3id.org/mixs/vocab/wall_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall location | +| **Mappings:** | | MIXS:0000843 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 142.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='north', description=None) | + diff --git a/mixs6/wall_surf_treatment.md b/mixs6/wall_surf_treatment.md new file mode 100644 index 00000000..34ceb675 --- /dev/null +++ b/mixs6/wall_surf_treatment.md @@ -0,0 +1,47 @@ + +# Slot: wall_surf_treatment + + +The surface treatment of interior wall + +URI: [mixs.vocab:wall_surf_treatment](https://w3id.org/mixs/vocab/wall_surf_treatment) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall surface treatment | +| **Mappings:** | | MIXS:0000845 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 144.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='paneling', description=None) | + diff --git a/mixs6/wall_texture.md b/mixs6/wall_texture.md new file mode 100644 index 00000000..64e84493 --- /dev/null +++ b/mixs6/wall_texture.md @@ -0,0 +1,47 @@ + +# Slot: wall_texture + + +The feel, appearance, or consistency of a wall surface + +URI: [mixs.vocab:wall_texture](https://w3id.org/mixs/vocab/wall_texture) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall texture | +| **Mappings:** | | MIXS:0000846 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 145.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='popcorn', description=None) | + diff --git a/mixs6/wall_thermal_mass.md b/mixs6/wall_thermal_mass.md new file mode 100644 index 00000000..672c3172 --- /dev/null +++ b/mixs6/wall_thermal_mass.md @@ -0,0 +1,48 @@ + +# Slot: wall_thermal_mass + + +The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + +URI: [mixs.vocab:wall_thermal_mass](https://w3id.org/mixs/vocab/wall_thermal_mass) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall thermal mass | +| **Mappings:** | | MIXS:0000222 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: joule per degree Celsius | +| | | Occurrence: 1 | +| | | Position: 146.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wall_water_mold.md b/mixs6/wall_water_mold.md new file mode 100644 index 00000000..fb0fc30c --- /dev/null +++ b/mixs6/wall_water_mold.md @@ -0,0 +1,47 @@ + +# Slot: wall_water_mold + + +Signs of the presence of mold or mildew on a wall + +URI: [mixs.vocab:wall_water_mold](https://w3id.org/mixs/vocab/wall_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall signs of water/mold | +| **Mappings:** | | MIXS:0000844 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 143.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='no presence of mold visible', description=None) | + diff --git a/mixs6/wastewater_type.md b/mixs6/wastewater_type.md new file mode 100644 index 00000000..12c14043 --- /dev/null +++ b/mixs6/wastewater_type.md @@ -0,0 +1,47 @@ + +# Slot: wastewater_type + + +The origin of wastewater such as human waste, rainfall, storm drains, etc. + +URI: [mixs.vocab:wastewater_type](https://w3id.org/mixs/vocab/wastewater_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wastewater type | +| **Mappings:** | | MIXS:0000353 | +| **Comments:** | | Expected value: wastewater type name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_content.md b/mixs6/water_content.md new file mode 100644 index 00000000..c4de331d --- /dev/null +++ b/mixs6/water_content.md @@ -0,0 +1,72 @@ + +# Slot: water_content + + +Water content measurement + +URI: [mixs.vocab:water_content](https://w3id.org/mixs/vocab/water_content) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [Sediment](Sediment.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water content | +| **Mappings:** | | MIXS:0000185 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per gram or cubic centimeter per cubic centimeter | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_content_soil_meth.md b/mixs6/water_content_soil_meth.md new file mode 100644 index 00000000..f91b5e6f --- /dev/null +++ b/mixs6/water_content_soil_meth.md @@ -0,0 +1,47 @@ + +# Slot: water_content_soil_meth + + +Reference or method used in determining the water content of soil + +URI: [mixs.vocab:water_content_soil_meth](https://w3id.org/mixs/vocab/water_content_soil_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water content method | +| **Mappings:** | | MIXS:0000323 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Occurrence: 1 | +| | | Position: 16.0 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_current.md b/mixs6/water_current.md new file mode 100644 index 00000000..4543e82c --- /dev/null +++ b/mixs6/water_current.md @@ -0,0 +1,60 @@ + +# Slot: water_current + + +Measurement of magnitude and direction of flow within a fluid + +URI: [mixs.vocab:water_current](https://w3id.org/mixs/vocab/water_current) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Water](Water.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water current | +| **Mappings:** | | MIXS:0000203 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per second, knots | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used in: 2 packages: miscellaneous natural or artificial environment, water | +| **Examples:** | | Example(value='10 cubic meter per second', description=None) | + diff --git a/mixs6/water_cut.md b/mixs6/water_cut.md new file mode 100644 index 00000000..18d6537e --- /dev/null +++ b/mixs6/water_cut.md @@ -0,0 +1,48 @@ + +# Slot: water_cut + + +Current amount of water (%) in a produced fluid stream; or the average of the combined streams + +URI: [mixs.vocab:water_cut](https://w3id.org/mixs/vocab/water_cut) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water cut | +| **Mappings:** | | MIXS:0000454 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 26.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_feat_size.md b/mixs6/water_feat_size.md new file mode 100644 index 00000000..3c063203 --- /dev/null +++ b/mixs6/water_feat_size.md @@ -0,0 +1,48 @@ + +# Slot: water_feat_size + + +The size of the water feature + +URI: [mixs.vocab:water_feat_size](https://w3id.org/mixs/vocab/water_feat_size) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water feature size | +| **Mappings:** | | MIXS:0000223 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 147.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_feat_type.md b/mixs6/water_feat_type.md new file mode 100644 index 00000000..adddf71a --- /dev/null +++ b/mixs6/water_feat_type.md @@ -0,0 +1,47 @@ + +# Slot: water_feat_type + + +The type of water feature present within the building being sampled + +URI: [mixs.vocab:water_feat_type](https://w3id.org/mixs/vocab/water_feat_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water feature type | +| **Mappings:** | | MIXS:0000847 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 148.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='stream', description=None) | + diff --git a/mixs6/water_production_rate.md b/mixs6/water_production_rate.md new file mode 100644 index 00000000..818be5d8 --- /dev/null +++ b/mixs6/water_production_rate.md @@ -0,0 +1,48 @@ + +# Slot: water_production_rate + + +Water production rates per well (e.g. 987 m3 / day) + +URI: [mixs.vocab:water_production_rate](https://w3id.org/mixs/vocab/water_production_rate) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water production rate | +| **Mappings:** | | MIXS:0000453 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per day | +| | | Occurrence: 1 | +| | | Position: 25.0 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_temp_regm.md b/mixs6/water_temp_regm.md new file mode 100644 index 00000000..0c934aa4 --- /dev/null +++ b/mixs6/water_temp_regm.md @@ -0,0 +1,48 @@ + +# Slot: water_temp_regm + + +Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:water_temp_regm](https://w3id.org/mixs/vocab/water_temp_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water temperature regimen | +| **Mappings:** | | MIXS:0000590 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Preferred unit: degree Celsius | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/watering_regm.md b/mixs6/watering_regm.md new file mode 100644 index 00000000..09c4e1fd --- /dev/null +++ b/mixs6/watering_regm.md @@ -0,0 +1,48 @@ + +# Slot: watering_regm + + +Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:watering_regm](https://w3id.org/mixs/vocab/watering_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | watering regimen | +| **Mappings:** | | MIXS:0000591 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Preferred unit: milliliter, liter | +| | | Occurrence: m | +| | | Position: 1.0 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/weekday.md b/mixs6/weekday.md new file mode 100644 index 00000000..22c1807d --- /dev/null +++ b/mixs6/weekday.md @@ -0,0 +1,47 @@ + +# Slot: weekday + + +The day of the week when sampling occurred + +URI: [mixs.vocab:weekday](https://w3id.org/mixs/vocab/weekday) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | weekday | +| **Mappings:** | | MIXS:0000848 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 149.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='Sunday', description=None) | + diff --git a/mixs6/weight_loss_3_month.md b/mixs6/weight_loss_3_month.md new file mode 100644 index 00000000..239aedd4 --- /dev/null +++ b/mixs6/weight_loss_3_month.md @@ -0,0 +1,48 @@ + +# Slot: weight_loss_3_month + + +Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + +URI: [mixs.vocab:weight_loss_3_month](https://w3id.org/mixs/vocab/weight_loss_3_month) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | weight loss in last three months | +| **Mappings:** | | MIXS:0000295 | +| **Comments:** | | Expected value: weight loss specification;measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 22.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes;5 kilogram', description=None) | + diff --git a/mixs6/wga_amp_appr.md b/mixs6/wga_amp_appr.md new file mode 100644 index 00000000..966b8ee8 --- /dev/null +++ b/mixs6/wga_amp_appr.md @@ -0,0 +1,35 @@ + +# Slot: wga_amp_appr + + +Method used to amplify genomic DNA in preparation for sequencing + +URI: [mixs.vocab:wga_amp_appr](https://w3id.org/mixs/vocab/wga_amp_appr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | WGA amplification approach | +| **Comments:** | | Expected value: enumeration | +| | | Position: 77.0 | +| **Examples:** | | Example(value='mda based', description=None) | + diff --git a/mixs6/wga_amp_kit.md b/mixs6/wga_amp_kit.md new file mode 100644 index 00000000..4ae3cadf --- /dev/null +++ b/mixs6/wga_amp_kit.md @@ -0,0 +1,35 @@ + +# Slot: wga_amp_kit + + +Kit used to amplify genomic DNA in preparation for sequencing + +URI: [mixs.vocab:wga_amp_kit](https://w3id.org/mixs/vocab/wga_amp_kit) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | WGA amplification kit | +| **Comments:** | | Expected value: kit name | +| | | Position: 78.0 | +| **Examples:** | | Example(value='qiagen repli-g', description=None) | + diff --git a/mixs6/win.md b/mixs6/win.md new file mode 100644 index 00000000..8282b4ba --- /dev/null +++ b/mixs6/win.md @@ -0,0 +1,59 @@ + +# Slot: win + + +A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + +URI: [mixs.vocab:win](https://w3id.org/mixs/vocab/win) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | well identification number | +| **Mappings:** | | MIXS:0000297 | +| **Comments:** | | Expected value: text | +| | | Occurrence: 1 | +| | | Position: 36.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wind_direction.md b/mixs6/wind_direction.md new file mode 100644 index 00000000..b6324fb3 --- /dev/null +++ b/mixs6/wind_direction.md @@ -0,0 +1,47 @@ + +# Slot: wind_direction + + +Wind direction is the direction from which a wind originates + +URI: [mixs.vocab:wind_direction](https://w3id.org/mixs/vocab/wind_direction) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wind direction | +| **Mappings:** | | MIXS:0000757 | +| **Comments:** | | Expected value: wind direction name | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='Northwest', description=None) | + diff --git a/mixs6/wind_speed.md b/mixs6/wind_speed.md new file mode 100644 index 00000000..6b9eeaf3 --- /dev/null +++ b/mixs6/wind_speed.md @@ -0,0 +1,48 @@ + +# Slot: wind_speed + + +Speed of wind measured at the time of sampling + +URI: [mixs.vocab:wind_speed](https://w3id.org/mixs/vocab/wind_speed) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wind speed | +| **Mappings:** | | MIXS:0000118 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter per second, kilometer per hour | +| | | Occurrence: 1 | +| | | Position: 1.0 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='21 kilometer per hour', description=None) | + diff --git a/mixs6/window_cond.md b/mixs6/window_cond.md new file mode 100644 index 00000000..4e161162 --- /dev/null +++ b/mixs6/window_cond.md @@ -0,0 +1,47 @@ + +# Slot: window_cond + + +The physical condition of the window at the time of sampling + +URI: [mixs.vocab:window_cond](https://w3id.org/mixs/vocab/window_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window condition | +| **Mappings:** | | MIXS:0000849 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 151.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='rupture', description=None) | + diff --git a/mixs6/window_cover.md b/mixs6/window_cover.md new file mode 100644 index 00000000..95ab1cf6 --- /dev/null +++ b/mixs6/window_cover.md @@ -0,0 +1,47 @@ + +# Slot: window_cover + + +The type of window covering + +URI: [mixs.vocab:window_cover](https://w3id.org/mixs/vocab/window_cover) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window covering | +| **Mappings:** | | MIXS:0000850 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 152.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='curtains', description=None) | + diff --git a/mixs6/window_horiz_pos.md b/mixs6/window_horiz_pos.md new file mode 100644 index 00000000..ad970e67 --- /dev/null +++ b/mixs6/window_horiz_pos.md @@ -0,0 +1,47 @@ + +# Slot: window_horiz_pos + + +The horizontal position of the window on the wall + +URI: [mixs.vocab:window_horiz_pos](https://w3id.org/mixs/vocab/window_horiz_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window horizontal position | +| **Mappings:** | | MIXS:0000851 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 153.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='middle', description=None) | + diff --git a/mixs6/window_loc.md b/mixs6/window_loc.md new file mode 100644 index 00000000..5ff2ffdf --- /dev/null +++ b/mixs6/window_loc.md @@ -0,0 +1,47 @@ + +# Slot: window_loc + + +The relative location of the window within the room + +URI: [mixs.vocab:window_loc](https://w3id.org/mixs/vocab/window_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window location | +| **Mappings:** | | MIXS:0000852 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 154.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='west', description=None) | + diff --git a/mixs6/window_mat.md b/mixs6/window_mat.md new file mode 100644 index 00000000..e381ba32 --- /dev/null +++ b/mixs6/window_mat.md @@ -0,0 +1,47 @@ + +# Slot: window_mat + + +The type of material used to finish a window + +URI: [mixs.vocab:window_mat](https://w3id.org/mixs/vocab/window_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window material | +| **Mappings:** | | MIXS:0000853 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 155.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/window_open_freq.md b/mixs6/window_open_freq.md new file mode 100644 index 00000000..46e7262e --- /dev/null +++ b/mixs6/window_open_freq.md @@ -0,0 +1,47 @@ + +# Slot: window_open_freq + + +The number of times windows are opened per week + +URI: [mixs.vocab:window_open_freq](https://w3id.org/mixs/vocab/window_open_freq) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window open frequency | +| **Mappings:** | | MIXS:0000246 | +| **Comments:** | | Expected value: value | +| | | Occurrence: 1 | +| | | Position: 156.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/window_size.md b/mixs6/window_size.md new file mode 100644 index 00000000..f0f12567 --- /dev/null +++ b/mixs6/window_size.md @@ -0,0 +1,48 @@ + +# Slot: window_size + + +The window's length and width + +URI: [mixs.vocab:window_size](https://w3id.org/mixs/vocab/window_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window area/size | +| **Mappings:** | | MIXS:0000224 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: inch, meter | +| | | Occurrence: 1 | +| | | Position: 150.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/window_status.md b/mixs6/window_status.md new file mode 100644 index 00000000..223ab0f1 --- /dev/null +++ b/mixs6/window_status.md @@ -0,0 +1,47 @@ + +# Slot: window_status + + +Defines whether the windows were open or closed during environmental testing + +URI: [mixs.vocab:window_status](https://w3id.org/mixs/vocab/window_status) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window status | +| **Mappings:** | | MIXS:0000855 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 158.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='open', description=None) | + diff --git a/mixs6/window_type.md b/mixs6/window_type.md new file mode 100644 index 00000000..1c71a8fc --- /dev/null +++ b/mixs6/window_type.md @@ -0,0 +1,47 @@ + +# Slot: window_type + + +The type of windows + +URI: [mixs.vocab:window_type](https://w3id.org/mixs/vocab/window_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window type | +| **Mappings:** | | MIXS:0000856 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 159.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='fixed window', description=None) | + diff --git a/mixs6/window_vert_pos.md b/mixs6/window_vert_pos.md new file mode 100644 index 00000000..b553ea42 --- /dev/null +++ b/mixs6/window_vert_pos.md @@ -0,0 +1,47 @@ + +# Slot: window_vert_pos + + +The vertical position of the window on the wall + +URI: [mixs.vocab:window_vert_pos](https://w3id.org/mixs/vocab/window_vert_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window vertical position | +| **Mappings:** | | MIXS:0000857 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 160.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='middle', description=None) | + diff --git a/mixs6/window_water_mold.md b/mixs6/window_water_mold.md new file mode 100644 index 00000000..3422efd7 --- /dev/null +++ b/mixs6/window_water_mold.md @@ -0,0 +1,47 @@ + +# Slot: window_water_mold + + +Signs of the presence of mold or mildew on the window. + +URI: [mixs.vocab:window_water_mold](https://w3id.org/mixs/vocab/window_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window signs of water/mold | +| **Mappings:** | | MIXS:0000854 | +| **Comments:** | | Expected value: enumeration | +| | | Occurrence: 1 | +| | | Position: 157.0 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='no presence of mold visible', description=None) | + diff --git a/mixs6/x_16s_recover.md b/mixs6/x_16s_recover.md new file mode 100644 index 00000000..b05bbeab --- /dev/null +++ b/mixs6/x_16s_recover.md @@ -0,0 +1,35 @@ + +# Slot: x_16s_recover + + +Can a 16S gene be recovered from the submitted SAG or MAG? + +URI: [mixs.vocab:x_16s_recover](https://w3id.org/mixs/vocab/x_16s_recover) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | 16S recovered | +| **Comments:** | | Expected value: boolean | +| | | Position: 63.0 | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/xylene.md b/mixs6/xylene.md new file mode 100644 index 00000000..7ea49f47 --- /dev/null +++ b/mixs6/xylene.md @@ -0,0 +1,60 @@ + +# Slot: xylene + + +Concentration of xylene in the sample + +URI: [mixs.vocab:xylene](https://w3id.org/mixs/vocab/xylene) + + +## Domain and Range + +None -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | xylene | +| **Mappings:** | | MIXS:0000156 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 84.0 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..1a3a849f --- /dev/null +++ b/requirements.txt @@ -0,0 +1,2 @@ +linkml + diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml new file mode 100644 index 00000000..780be34c --- /dev/null +++ b/src/schema/mixs.yaml @@ -0,0 +1,32 @@ +id: http://w3id.org/mixs +name: MIxS +description: Minimal Information about any Sequence Standard +imports: +- linkml:types +- checklists +- core +- air +- built_environment +- host_associated +- human_associated +- human_gut +- human_oral +- human_skin +- human_vaginal +- hydrocarbon_resources_cores +- hydrocarbon_resources_fluids_swabs +- microbial_mat_biofilm +- miscellaneous_natural_or_artificial_environment +- plant_associated +- sediment +- soil +- wastewater_sludge +- water +prefixes: + linkml: https://w3id.org/linkml/ + mixs.vocab: https://w3id.org/mixs/vocab/ + MIXS: https://w3id.org/mixs/terms/ +default_prefix: mixs.vocab +slots: {} +classes: {} +subsets: {}