| Category | MIXS ID | Metadata field | Brief description | Definition | Example of Annotation | Source |
|---|---|---|---|---|---|---|
| Sample metadata | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”] | collected_by | Who collected the sample | Name of person or institute that collected the sample | Charité – Universitätsmedizin Berlin | |
| [MIXS:0000001] | sample_size/mass | Amount or size of the collected sample | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected | 2 g | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” | |
| [MIXS:0000011] | collection_date | Date at which the sample was collected | The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated. Restricted text field, [ISO8601] compliant | 2008-01-23T19:23:10+00:00 | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” | |
| [MIXS:0000092] | project_name | project name under which sampling and sequencing was done | Name of the project within which the sequencing was organized | Canine–Human Household Gut Microbiome Study | ||
| [MIXS:0000110] | samp_store_temp | Temperature at which the sample was stored | Temperature at which sample was stored, e.g. -80 degree Celsius | -80˚C | ||
| [MIXS:0000113] | temp | temperature | Temperature of the sample at the time of sampling | 37˚C | ||
| [MIXS:0000752] | misc_param | miscellaneous parameter | Any other measurement performed or parameter collected, that is not listed here | probiotic use: yes (Bifidobacterium longum, 10⁹ CFU/day) | ||
| [MIXS:0000754] | perturbation | perturbation | Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types | Amoxicillin [CHEBI:2676]; 500 mg orally, 3× day for 7 days | ||
| [MIXS:0001107] | samp_name | Identifier of sample obtained from sampled host | A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name | P001_stool_20250203 | ||
| [MIXS:0001216] | microb_cult_med | Microbiological culture medium (applicable only if microorganism can be cultivated) | Composition of processed material providing the needed nourishment for microorganisms or cells to grow in vitro. This field accepts terms listed under culture medium [OBI:0000079]. If the proper descriptor is not listed please use text to describe the culture medium | brain heart infusion medium [MICRO:0000569] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, MSI-ECWSG (Morrison et al. (2007)) | |
| [MIXS:0001320] | samp_taxon_id | Taxonomical identifier of sample | NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use ‘synthetic metagenome for mock community/positive controls, or ’blank sample’ for negative controls. Expected_value: [NCBI taxonomy ID] | Gut Metagenome [NCBITaxon:749906] | “GSC MIXS: MIMAG”, “GSC MIXS: MIGSBacteria”, “GSC MIMS: Metagenome or Environmental”, “Minimum Information about a Single Ampligied Genome (MiSAG)”, “Minimum Information about an Uncultivated Virus Genome (Miuvig)” | |
| [] | microbial_isolate | microbial isolate cultured?: Y/N | Y | |||
| Site metadata | [MIXS:0000009] | lat_lon | geographic location (latitude and longitude) | The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees, limited to 8 decimal points, and in WGS84 system | 52.526396, 13.376270 | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” |
| [MIXS:0000010] | geo_loc_name | geographic location (country and/or sea,region) | The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the [INSDC country list], or the [GAZ ontology] | Germany: Berlin [GAZ:00003510] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”) | |
| [MIXS:0000012] | env_broad_scale | Broad-scale environmental context | Report the major environmental system the sample or specimen came from. Systems(s) identifiers should provide a coarse, general environmental context of where the sampling was done. Terms, such as anatomical sites, from [OBO Library] ontologies which interoperate with EnvO (e.g. [[[[UBERON\]]]](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, | should be used to separate them. | urban biome [ENVO:01000249] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” | |
| [MIXS:0000013] | env_local_scale | Local-scale environmental context | Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Entry should be of a smaller environmental context than env_broad_scale. Terms, such as anatomical sites, from other [OBO Library] ontologies which interoperate with EnvO (e.g. [[[[UBERON\]]]](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, | should be used to separate them. | household environment [ENVO:03501339]|digestive tract [] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” | |
| [MIXS:0000014] | env_medium | Environmental medium | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. Terms from other [OBO ontologies] are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). If more than one term applies to the field, | should be used to separate them. | fecal material [ENVO:00002003] | “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” | |
| [MIXS:0000093] | elev | elevation | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | 34 m | “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”) | |
| [MIXS:0000094] | alt | altitude | Altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit | Not applicable | “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” | |
| Site/host metadata | [MIXS:0000751] | chem_administration | List of chemical administered to sampled host or site | List of chemical compounds administered to host or on site where sampling occurred. Can include multiple compounds separated by |. For compounds consult [chemical entities of biological interest ontology (chebi) (v 163)] | amoxicillin [CHEBI:2676], 500 mg | “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS” |
| Host metadata | [MIXS:0000031] | disorder_history | Disorder history of sampled host | Terms from [DOID ontologies] should be used to describe disorder. Host history of pulmonary [[[[DOID:850\]]]](http://purl.obolibrary.org/obo/DOID_850), nose-throat [[[[DOID:974\]]]](http://purl.obolibrary.org/obo/DOID_974), blood [[[[DOID:74\]]]](http://purl.obolibrary.org/obo/DOID_74), kidney [[[[DOID:557\]]]](http://purl.obolibrary.org/obo/DOID_557) and urogenital tract disorders [[[[DOID:18\]]]](http://purl.obolibrary.org/obo/DOID_18) . If multiple disorders apply, separate them by | | lung abscess [[[[DOID:0060317\]]]](http://purl.obolibrary.org/obo/DOID_0060317)|tonsillitis [[[[DOID:10456\]]]](http://purl.obolibrary.org/obo/DOID_10456)|hypochromic anemia [[[[DOID:11759\]]]](http://purl.obolibrary.org/obo/DOID_11759) | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “U.s. Office of Management and Budget (OMB): About the Topic of Race” |
| [MIXS:0000031] | host_disease_stat | Disease status of the sampled host | Diagnosed diseases of host; can hold multiple values, separated by |. Non-human host diseases should be deposited as free text | Streptococcus pneumonia [DOID:0040084] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS” | |
| [MIXS:0000248] | host_common_name | Common name of the sampled host | Common name of the host | human | “GSC MIxS: Host-associatedMIMS” | |
| [MIXS:0000250] | host_taxid | Taxonomy identifier of sampled host | Scientific name [[[[NCBI taxonomy ID\]]]](https://www.ncbi.nlm.nih.gov/taxonomy) | Homo sapiens [[[[NCBI:txid9606\]]]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock) | MSI-ECWSG (Morrison et al. (2007)) | |
| [MIXS:0000255] | host_age | Age of sampled host | Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees | 28 y | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” | |
| [MIXS:0000262] | smoker | smoker | Specification of smoking status | Current Some Day Smoker [NCIT:C67146] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: MimsHumanAssociated” | |
| [MIXS:0000263] | host_tot_mass | Total mass of the sampled host | Total mass of the host at collection, the unit depends on host | 78 kg | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” | |
| [MIXS:0000264] | host_height | Height of sampled host | Height of host or length of host | 180 cm | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” | |
| [MIXS:0000267] | pet_farm_animal | presence of pets or farm animals around sampled host | Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present | Canis lupus familiaris [NCBI:txid9615] | ||
| [MIXS:0000274] | host_body_temp | Body temperature of sampled host | Core body temperature of the host when sample was collected | 36.8˚C | ||
| [MIXS:0000285] | sexual_act | sexual activity of sampled host | Current sexual partner and frequency of sex | monogamous partner, 2 times/week | ||
| [MIXS:0000317] | host_body_mass_index | body-mass index of sampled host | Body mass index, calculated as weight/(height)squared | 24.1 kg/m² | ||
| [MIXS:0000365] | host_genotype | host genotype | Observed genotype | Not determined | ||
| [MIXS:0000811] | host_sex | Gender of sampled host | Gender sex of the sampled host Gender [NCIT:C17357] | agender [NCIT:C205469] | ||
| [MIXS:0000861] | host_subject_id | anonymised identifier of sampled host | A unique identifier by which each subject can be referred to, de-identified | su9sa8 | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal” | |
| [MIXS:0000862] | urobiom_sex | Physical sex of sampled host | Physical sex of the host as Sex assigned at birth [NCIT:C205472] | Assigned Female at Birth [NCIT:C205474] | ||
| [MIXS:0000867] | host_body_site | Sampled body site of the host | Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc…). Recomended use of [FMA] or [UBERON] ontologies | Colon [UBERON:0001155] | “GSC MIxS: Host-associatedMIMS”, “ENA Host Associated Checklist; Checklist: ERC000013”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS” | |
| [MIXS:0000866] | host_body_habitat | Body habitat from which the sample was obtained from | Original body habitat where the sample was obtained from | Digestive tract [UBERON:0001555] | ||
| [MIXS:0000869] | host_diet | Diet of sampled host | Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types | omnivore [[[[ecocore:00000082\]]]](http://purl.obolibrary.org/obo/ecocore_00000082) | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” | |
| [MIXS:0000874] | host_phenotype | Identified phenotype of sampled host | Phenotype of human or other host. Use terms from the phenotypic quality ontology [(PATO)] or the Human Phenotype Ontology [(HP)] | BCL2 expression [HP:0430092] | ||
| [MIXS:0000888] | host_body_product | Body product that was examined and sampled from host | Bodily substance where the sample was obtained from. Recomended use of [FMA] or [UBERON] ontologies. Multiple ontologies can apply, use | to separate them | Feces [UBERON:0001988] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal” | |
| [MIXS:0000895] | ethnicity | ethnicity | A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. | German | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “U.s. Office of Management and Budget (OMB): About the Topic of Race”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal” | |
| [MIXS:0000896] | host_occupation | Occupation of the sampled host | Most frequent job performed by subject | Nursery nurse [SNOMED:224578004] | ||
| [MIXS:0000905] | special_diet | special diet of the sampled host | Specification of special diet; can include multiple special diets | Ketogenic diet [SNOMED:765060000] |
Human Disease Ontology - DOID - The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.
Human Phenotype Ontology - HP - The Human Phenotype Ontology provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease.
Uber-anatomy ontology - UBERON - Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
Foundational Model of Anatomy Ontology - FMA - The FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species. The Foundational Model of Anatomy (FMA) ontology is one of the information resources integrated in the distributed framework of the Anatomy Information System developed and maintained by the Structural Informatics Group at the University of Washington.
SNOMED Clinical Terms (International Edition) - SNOMED CT or SNOMED Clinical Terms is a systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.
Neuro Behavior Ontology - NBO - An ontology of human and animal behaviours and behavioural phenotypes.
The BRENDA Tissue Ontology - BTO - A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.
Gene Ontology - GO - The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.
Chemical Entities of Biological Interest - ChEBI - An open-access database and ontology of chemical entities. The chemical entities in ChEBI are either naturally occurring molecules or synthetic compounds used to intervene in the processes of living organisms. ChEBI uses the nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). ChEBI also incorporates an ontological classification, whereby the relationships between chemical entities or classes of entities and their parents and/or children are defined; this enables queries based for example on chemical class and role.
National Ccancer Institute Thesaurus - NCIT - NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.
“ENA Marine Microalgae Checklist; Checklist: ERC000043.” https://www.ebi.ac.uk/ena/browser/view/ERC000043.
“GOLD Ecosystem Classification Paths.” https://gold.jgi.doe.gov/ecosystem_classification.
“GSC MIxS Human Associated; ENA Checklist: ERC000014.” https://www.ebi.ac.uk/ena/browser/view/ERC000014.
“GSC MIxS: Host-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/.
“GSC MIxS: Human-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/.
“GSC MIxS: Human-gutMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-gutMIMS/.
“GSC MIxS: Human-oralMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-oralMIMS/.
“GSC MIxS: Human-skinMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-skinMIMS/.
“GSC MIxS: Human-vaginalMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-vaginalMIMS/.
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package.” https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/.
Morrison, Norman, Daniel Bearden, Jacob G. Bundy, Timothy Collette, Fraser Currie, Matthew Davey, Migdalia Dominguez, et al. 2007. “Standard Reporting Requirements for Biological Samples in Metabolomics Experiments: Environmental Context.” Metabolomics 3 (2): 203–10. https://doi.org/10.1007/s11306-007-0067-1.
“U.s. Office of Management and Budget (OMB): About the Topic of Race.” https://www.census.gov/topics/population/race/about.html.