Item.md

Item

Properties

Name	Type	Description	Notes
schema_version	str	The version of the JSON schema that the server uses to validate the object.	[optional]
uuid	str	The unique identifier associated with every object.	[optional]
notes	str	DACC internal notes.	[optional]
aliases	List[str]	Lab specific identifiers to reference an object.	[optional]
creation_timestamp	str	The date the object was created.	[optional]
submitted_by	str	The user who submitted the object.	[optional]
submitter_comment	str	Additional information specified by the submitter to be displayed as a comment on the portal.	[optional]
description	str	A plain text description of the object.	[optional]
status	str	The status of the metadata object.	[optional]
user	str	The user that is assigned to this access key.	[optional]
access_key_id	str	An access key.	[optional]
secret_access_key_hash	str	A secret access key.	[optional]
id	str		[optional]
type	List[str]		[optional]
summary	str	A summary of the object.	[optional]
release_timestamp	str	The date the object was released.	[optional]
lab	str	Lab associated with the submission.
award	str	Grant associated with the submission.
analysis_step_types	List[str]	The classification of the software.	[optional]
step_label	str	Unique lowercased label of the analysis step that includes the relevant assays, the software used, and the purpose of the step, e.g. rampage-grit-peak-calling-step	[optional]
title	str	The full name of the user.	[optional]
workflow	str	The computational workflow in which this analysis step belongs.	[optional]
parents	List[str]	The precursor steps.	[optional]
input_content_types	List[str]	The content types used as input for the analysis step.	[optional]
output_content_types	List[str]	The content types produced as output by the analysis step.	[optional]
name	str	The preferred viewable name of the workflow.	[optional]
analysis_step	str	The analysis step which this version belongs to.	[optional]
software_versions	List[str]	The software versions used in this analysis step versions.	[optional]
url	str	An external resource with additional information.	[optional]
start_date	str	The date when the award begins.	[optional]
end_date	str	The date when the award concludes.	[optional]
pis	List[str]	Principal Investigator(s) of the grant.	[optional]
contact_pi	str	The contact Principal Investigator of the grant.	[optional]
project	str	The collection of biological data related to a single initiative, originating from a consortium.	[optional]
viewing_group	str	The group that determines which set of data the user has permission to view.	[optional]
component	str	The project component the award is associated with.	[optional]
classification	str	Sample specific biomarker.	[optional]
quantification	str	The biomarker association to the biosample, disease or other condition. This can be the absence of the biomarker or the presence of the biomarker in some low, intermediate or high quantity.	[optional]
synonyms	List[str]	Synonyms for the term that have been recorded in an ontology.	[optional]
gene	List[str]	ENSEMBL GeneID of official nomenclature approved gene. The GeneID does not include the current version number suffix.	[optional]
name_quantification	str	A concatenation of the name and quantification of the biomarker.	[optional]
biomarker_for	List[str]	The samples which have been confirmed to have this biomarker.	[optional]
attachment	Attachment		[optional]
document_type	str	The category that best describes the document.	[optional]
characterization_method	str	The method used for the characterization.	[optional]
urls	List[str]	Link to the institutional certification form.	[optional]
taxa	str	The species of the organism.	[optional]
publication_identifiers	List[str]	The publication identifiers that provide more information about the object.	[optional]
documents	List[str]	Documents that provide additional information (not data file).	[optional]
accession	str	A unique identifier to be used to reference the object prefixed with PKB.	[optional]
alternate_accessions	List[str]	Accessions previously assigned to objects that have been merged with this object.	[optional]
collections	List[str]	Some samples are part of particular data collections.	[optional]
revoke_detail	str	Explanation of why an object was transitioned to the revoked status.	[optional]
dbxrefs	List[str]	Biosample identifiers from external resources, such as Biosample database or Cellosaurus.	[optional]
sex	str		[optional]
phenotypic_features	List[str]	A list of associated phenotypic features of the donor.	[optional]
virtual	bool	Virtual samples are not representing actual physical entities from experiments, but rather capturing metadata about hypothetical samples that the reported analysis results are relevant for.	[optional]
ethnicities	List[str]	Self-Reported Ethnicity of the donor.	[optional]
genetic_ethnicities	List[str]	Inferred ancestry of the donor from genetic analysis	[optional]
living_donor	bool	Living Donor	[optional]
family_history_of_diabetes	str	Family History of Diabetes	[optional]
family_history_of_diabetes_relationship	List[str]	Family History of Diabetes Relationship.	[optional]
rrid	str	Research Unique Identifier. PanKbase will only take donors with RRID	[optional]
pancreas_tissue_available	bool	Pancreas tissue is available for research or analysis	[optional]
center_donor_id	str	Donor center ID identifier for cross-referencing	[optional]
biological_sex	str	Inferred biological sex derived from genomic data	[optional]
age	str	Age of organism at the time of collection of the sample.	[optional]
bmi	float	Body mass index (Kg/m2)	[optional]
diabetes_duration	str	Diabetes Duration in years	[optional]
diabetes_status	List[str]	Diabetes status T1D,T2D,MODY, etc. MONDO ontology term	[optional]
diabetes_status_description	str	Description of diabetes status	[optional]
hba1c	float	The percentage measurement of HbA1c, which reflects the average blood glucose levels over the past 2-3 months. If not available, 'NA'	[optional]
diabetes_status_hba1c	str	A categorization of diabetes status based on adjusted HbA1C levels, considering factors such as age, race, or other clinical conditions that might influence HbA1C measurements	[optional]
donation_type	str	The type of organ donation, categorized as DCD, NDD, or MAID	[optional]
cause_of_death	str	The primary medical condition or event that led to the patient’s death	[optional]
c_peptide	float	The concentration of C-Peptide in the blood, a marker used to assess insulin production and pancreatic function	[optional]
aab_gada	bool	The presence of Autoantibodies against GADA	[optional]
aab_gada_value	float	AAB GADA value (unit/ml)	[optional]
aab_ia2	bool	The presence of Autoantibodies against IA2	[optional]
aab_ia2_value	float	AAB IA2 value (unit/ml)	[optional]
aab_znt8	bool	The presence of Autoantibodies against ZNT8	[optional]
aab_znt8_value	float	AAB ZNT8 value (unit/ml)	[optional]
hla_typing	List[str]	Series of comma-separated values describing HLA types as: class, locus, allele1, allele2, method	[optional]
other_tissues_available	List[str]	Tissues obtained from the donor	[optional]
hospital_stay	float	The total number of days the patient was hospitalized	[optional]
glucose_loweing_theraphy	List[str]	Details the type of therapy or medication regimen the patient is on to manage blood glucose levels, including oral medications, insulin, or other treatments.	[optional]
human_donor_identifiers	List[str]	Identifiers of this human donor.	[optional]
sources	List[str]	The originating lab(s) or vendor(s).	[optional]
lot_id	str	The lot identifier provided by the originating lab or vendor.	[optional]
product_id	str	The product identifier provided by the originating lab or vendor.	[optional]
strain_background	str	The specific parent strain designation of a non-human donor.	[optional]
strain	str	The specific strain designation of a non-human donor.	[optional]
genotype	str	The genotype of the strain according to accepted nomenclature conventions.	[optional]
individual_rodent	bool	This rodent donor represents an individual rodent.	[optional]
rodent_identifier	str	The identifier for this individual rodent donor.	[optional]
controlled_access	bool	Indicator of whether the samples are under controlled access.	[optional]
anvil_url	str	URL linking to the controlled access file that has been deposited at AnVIL workspace.	[optional]
transcriptome_annotation	str	The annotation and version of the reference resource.	[optional]
assembly	str	Genome assembly applicable for the tabular data.	[optional]
reference_files	List[str]	Link to the reference files used to generate this file.	[optional]
analysis_step_version	str	The analysis step version of the file.	[optional]
content_md5sum	str	The MD5sum of the uncompressed file.	[optional]
content_type	str	The type of content in the file.	[optional]
derived_from	List[str]	The files participating as inputs into software to produce this output file.	[optional]
file_format	str	The file format or extension of the file.	[optional]
file_format_specifications	List[str]	Document that further explains the file format.	[optional]
file_set	str	The file set that this file belongs to.	[optional]
file_size	int	File size specified in bytes.	[optional]
md5sum	str	The md5sum of the file being transferred.	[optional]
submitted_file_name	str	Original name of the file.	[optional]
upload_status	str	The upload/validation status of the file.	[optional]
validation_error_detail	str	Explanation of why the file failed the automated content checks.	[optional]
redacted	bool	Indicates whether the alignments data have been sanitized (redacted) to prevent leakage of private and potentially identifying genomic information.	[optional]
filtered	bool	Indicates if the signal file is filtered.	[optional]
integrated_in	List[str]	Construct library set(s) that this file was used for in insert design.	[optional]
input_file_for	List[str]	The files which are derived from this file.	[optional]
gene_list_for	List[str]	File Set(s) that this file is a gene list for.	[optional]
loci_list_for	List[str]	File Set(s) that this file is a loci list for.	[optional]
href	str	The download path to obtain file.	[optional]
s3_uri	str	The S3 URI of public file object.	[optional]
upload_credentials	object	The upload credentials for S3 to submit the file content.	[optional]
content_summary	str	A summary of the data in the signal file.	[optional]
seqspec_of	List[str]	Sequence files this file is a seqspec of.	[optional]
file_format_type	str	The subtype of bed files.	[optional]
dimension1	str	First dimension of the matrix.	[optional]
dimension2	str	Second dimension of the matrix.	[optional]
source_url	str	An external resource to the code base of the workflow in github.	[optional]
external	bool	Indicates whether the file was obtained from an external, non-IGVF source.	[optional]
external_id	str	A unique identifier for the file at its original source.	[optional]
flowcell_id	str	The alphanumeric identifier for the flowcell of a sequencing machine.	[optional]
lane	int	An integer identifying the lane of a sequencing machine.	[optional]
read_count	int	Number of reads in a fastq file.	[optional]
minimum_read_length	int	For high-throughput sequencing, the minimum number of contiguous nucleotides determined by sequencing.	[optional]
maximum_read_length	int	For high-throughput sequencing, the maximum number of contiguous nucleotides determined by sequencing.	[optional]
mean_read_length	float	For high-throughput sequencing, the mean number of contiguous nucleotides determined by sequencing.	[optional]
sequencing_platform	str	The measurement device used to produce sequencing data.	[optional]
sequencing_kit	str	A reagent kit used with a library to prepare it for sequencing.	[optional]
sequencing_run	int	An ordinal number indicating which sequencing run of the associated library that the file belongs to.	[optional]
illumina_read_type	str	The read type of the file. Relevant only for files produced using an Illumina sequencing platform.	[optional]
index	str	An Illumina index associated with the file.	[optional]
seqspecs	List[str]	Link(s) to the associated seqspec YAML configuration file(s).	[optional]
strand_specificity	str	The strandedness of the signal file: plus, minus, or unstranded.	[optional]
normalized	bool	Indicates if the signal file is normalized.	[optional]
start_view_position	str	The 0-based coordinate for the default starting position when viewing the signal in a genome browser.	[optional]
input_file_sets	List[str]	The file set(s) required for this prediction set.	[optional]
samples	List[str]	Samples covered by this institutional certificate.
donors	List[str]	Donor(s) the sample was derived from.
file_set_type	str	The category that best describes this prediction set.
files	List[str]	The files associated with this file set.	[optional]
control_for	List[str]	The file sets for which this file set is a control.	[optional]
submitted_files_timestamp	str	The timestamp the first file object in the file_set or associated auxiliary sets was created.	[optional]
input_file_set_for	List[str]	The file sets that use this file set as an input.	[optional]
assay_titles	List[str]	Title(s) of assays that produced data analyzed in the analysis set.	[optional]
library_construction_platform	str	The platform used to construct the library sequenced in this measurement set.	[optional]
measurement_sets	List[str]	The measurement sets that link to this auxiliary set.	[optional]
small_scale_loci_list	List[object]	A small scale (<=100) list of specific chromosomal region(s).	[optional]
large_scale_loci_list	str	A large scale list (>100) of specific chromosomal regions.	[optional]
small_scale_gene_list	List[str]	The specific, small scale list of (<=100) gene(s) this prediction set targets.	[optional]
large_scale_gene_list	str	The large scale list of (>100 genes) this this prediction set targets.	[optional]
scope	str	The scope or scale that this prediction set is designed to target. If the scope is across gene(s) or loci, these will need to be specified in the genes or loci property.	[optional]
selection_criteria	List[str]	The criteria used to select the sequence material cloned into the library.	[optional]
integrated_content_files	List[str]	The files containing sequence material of interest either used for insert design or directly cloned into vectors in this library.	[optional]
associated_phenotypes	List[str]	Ontological terms for diseases or phenotypes associated with the sequence material cloned in this construct library.	[optional]
orf_list	List[str]	List of Open Reading Frame this construct library was designed to target.	[optional]
exon	str	An identifier in plain text for the specific exon in an expression vector library. The associated gene must be listed in the small_scale_gene_list property.	[optional]
tile	Tile		[optional]
guide_type	str	The design of guides used in a CRISPR library, paired-guide (pgRNA) or single-guide (sgRNA).	[optional]
tiling_modality	str	The tiling modality of guides across elements or loci in a CRISPR library.	[optional]
average_guide_coverage	float	The average number of guides targeting each element of interest in the library.	[optional]
lower_bound_guide_coverage	int	Lower bound of the number of guides targeting each element of interest in the library.	[optional]
upper_bound_guide_coverage	int	Upper bound of the number of guides targeting each element of interest in the library.	[optional]
average_insert_size	float	The average size of the inserts cloned into vectors in the library.	[optional]
lower_bound_insert_size	int	Lower bound of the size of the inserts cloned in vectors in the library.	[optional]
upper_bound_insert_size	int	Upper bound of the size of the inserts cloned in vectors in the library.	[optional]
targeton	str	An identifier in plain text for the specific targeton in an editing template library. The associated gene must be listed in the small_scale_gene_list property.	[optional]
applied_to_samples	List[str]	The samples that link to this construct library set.	[optional]
assemblies	List[str]	The genome assemblies to which the referencing files in the file set are utilizing (e.g., GRCh38).	[optional]
transcriptome_annotations	List[str]	The annotation versions of the reference resource.	[optional]
assay_term	str	The assay used to produce data in this measurement set.	[optional]
protocols	List[str]	Links to the protocol(s) for preparing the samples on Protocols.io.	[optional]
preferred_assay_title	str	The custom lab preferred label for the experiment performed in this measurement set.	[optional]
multiome_size	int	The number of datasets included in the multiome experiment this measurement set is a part of.	[optional]
control_file_sets	List[str]	File sets that can serve as scientific controls for this measurement_set.	[optional]
sequencing_library_types	List[str]	Description of the libraries sequenced in this measurement set.	[optional]
auxiliary_sets	List[str]	The auxiliary sets of files produced alongside raw data from this measurement set.	[optional]
external_image_url	str	Links to the external site where images produced by this measurement are stored.	[optional]
targeted_genes	List[str]	A list of genes targeted in this assay. For example, TF ChIP-seq attempts to identify binding sites of a protein encoded by a specific gene. In CRISPR FlowFISH, the modified samples are sorted based on expression of a specific gene. This property differs from small_scale_gene_list in Construct Library Set, which describes genes targeted by the content integrated in the constructs (such as guide RNAs.)	[optional]
related_multiome_datasets	List[str]	Related datasets included in the multiome experiment this measurement set is a part of.	[optional]
model_name	str	The custom lab name given to this predictive model set.	[optional]
model_version	str	The semantic version number for this predictive model set.	[optional]
prediction_objects	List[str]	The objects this predictive model set is targeting.	[optional]
model_zoo_location	str	The link to the model on the Kipoi repository.	[optional]
software_version	str	Version of software used for the derivation of this model set.	[optional]
geneid	str	ENSEMBL GeneID of official nomenclature approved gene. The GeneID does not include the current version number suffix.	[optional]
symbol	str	Gene symbol approved by the official nomenclature.	[optional]
locations	List[GeneLocation1]	Gene locations specified using 1-based, closed coordinates for different versions of reference genome assemblies.	[optional]
version_number	str	Current ENSEMBL GeneID version number of the gene.	[optional]
geneid_with_version	str	The ENSEMBL GeneID concatenated with its version number.	[optional]
caption	str	The caption of the image.	[optional]
thumb_nail	str	Image url	[optional]
download_url	str	Download Url	[optional]
certificate_identifier	str	A unique identifier for the certificate.	[optional]
data_use_limitation	str	Code indicating the limitations on data use for data generated from the applicable samples. GRU (General research use): Use of the data is limited only by the terms of the Data Use Certification: these data will be added to the dbGaP Collection. HMB (Health/medical/biomedical): Use of the data is limited to health/medical/biomedical purposes, does not include the study of population origins or ancestry. DS (Disease specific): Use of the data must be related to the specified disease. Other: any other customized limitation.	[optional]
data_use_limitation_modifiers	List[str]	Code indicating a modifier on the limitations on data use for data generated from the applicable samples. COL: Requestor must provide a letter of collaboration with the primary study investigator(s). GSO: Use of the data is limited to genetic studies only. IRB: Approval Required IRB Requestor must provide documentation of local IRB approval. MDS: Use of the data includes methods development research (e.g., development and testing of software or algorithms). NPU: Use of the data is limited to not-for-profit organizations. PUB: Requestor agrees to make results of studies using the data available to the larger scientific community.	[optional]
pi	str	Principle Investigator of the lab.	[optional]
awards	List[str]	Grants associated with the lab.	[optional]
institute_label	str	An abbreviation for the institute the lab is associated with.	[optional]
cas	str	The name of the CRISPR associated protein used in the modification.	[optional]
fused_domain	str	The name of the molecule fused to a Cas protein.	[optional]
modality	str	The purpose or intended effect of a CRISPR modification.	[optional]
tagged_protein	str	The tagged protein in modifications in which the Cas nuclease is fused to an antibody.	[optional]
cas_species	str	The originating species of the Cas nuclease.	[optional]
activated	bool	A boolean indicating whether the modification has been activated by a chemical agent.	[optional]
activating_agent_term_id	str	The CHEBI identifier for the activating agent of the modification.	[optional]
activating_agent_term_name	str	The CHEBI name for the activating agent of the modification.	[optional]
biosamples_modified	List[str]	The biosamples which have been modified with this modification.	[optional]
term_id	str	An ontology identifier describing a biological sample	[optional]
term_name	str	Ontology term describing a biological sample, assay, trait, or disease.	[optional]
deprecated_ntr_terms	List[str]	A list of deprecated NTR terms previously associated with this ontology term.	[optional]
is_a	List[str]	A list of ontology terms which are the nearest ancestor to this ontology term.	[optional]
preferred_assay_titles	List[str]	The custom lab preferred labels that this assay term may be associated with.	[optional]
ancestors	List[str]	List of term names of ontological terms that precede the given term in the ontological tree. These ancestor terms are typically more general ontological terms under which the term is classified.	[optional]
ontology	str	The ontology in which the term is recorded.	[optional]
assay_slims	List[str]	A broad categorization of the assay term.	[optional]
category_slims	List[str]	The type of feature or interaction measured by the assay.	[optional]
objective_slims	List[str]	The purpose of the assay.	[optional]
company	str	The company that developed and sells the instrument.	[optional]
sequencing_kits	List[str]	The available sequencing kits for this platform.	[optional]
organ_slims	List[str]	Organs associated with the sample term.	[optional]
cell_slims	List[str]	Cells associated with the sample term.	[optional]
developmental_slims	List[str]	Developmental stages associated with the sample term.	[optional]
system_slims	List[str]	Organ systems associated with the sample term.	[optional]
orf_id	str	Open reading frame ID.	[optional]
protein_id	str	ENSEMBL ProteinID of official nomenclature approved protein. The ProteinID does not include the current version number suffix.	[optional]
pct_identical_protein	float	The percentage of identical matches to Ensembl protein.	[optional]
pct_coverage_protein	float	The percentage of ORF covered by Ensembl protein.	[optional]
pct_coverage_orf	float	The percentage of Ensembl protein covered by ORF.	[optional]
parent	str	The parent page associated with this page.	[optional]
layout	PageLayout		[optional]
canonical_uri	str	The path of the page.	[optional]
feature	str	The phenotypic feature observed for the donor.	[optional]
quantity	float	A quantity associated with the phenotypic feature, if applicable.	[optional]
quantity_units	str	The unit of measurement for a quantity associated with the phenotypic feature.	[optional]
observation_date	str	The date the feature was observed or measured.	[optional]
abstract	str	Abstract of the publication or communication.	[optional]
authors	str	The authors of the publication.	[optional]
date_published	str	The date the publication or communication was published; must be in YYYY-MM-DD format.	[optional]
date_revised	str	The date the publication was revised.	[optional]
issue	str	The issue of the publication.	[optional]
page	str	Pagination of the reference	[optional]
volume	str	The volume of the publication.	[optional]
journal	str	The journal of the publication.	[optional]
published_by	List[str]	The affiliation of the lab with a larger organization, such as IGVF.	[optional]
publication_year	int	The year the publication was published.	[optional]
lower_bound_age	float	Lower bound of age of the organism at the time of collection of the sample.	[optional]
upper_bound_age	float	Upper bound of age of the organism at the time of collection of the sample.	[optional]
age_units	str	The units of time associated with age of the biosample.	[optional]
sample_terms	List[str]	Ontology terms identifying a biosample.	[optional]
disease_terms	List[str]	Ontology term of the disease associated with the biosample.	[optional]
pooled_from	List[str]	The biosamples this biosample is pooled from.	[optional]
part_of	str	Links to a biosample which represents a larger sample from which this sample was taken regardless of whether it is a tissue taken from an organism or smaller slices of a piece of tissue or aliquots of a cell growth.	[optional]
originated_from	str	Links to a biosample that was originated from due to differentiation, dedifferentiation, reprogramming, or the introduction of a genetic modification.	[optional]
treatments	List[str]	A list of treatments applied to the biosample with the purpose of perturbation.	[optional]
biomarkers	List[str]	Biological markers that are associated with this sample.	[optional]
embryonic	bool	Biosample is embryonic.	[optional]
modifications	List[str]	Links to modifications applied to this biosample.	[optional]
cellular_sub_pool	str	Cellular sub-pool fraction of the sample. Also known as PKR and sub-library.	[optional]
starting_amount	float	The initial quantity of samples obtained.	[optional]
starting_amount_units	str	The units used to quantify the amount of samples obtained.	[optional]
date_obtained	str	The date the sample was harvested, dissected or created, depending on the type of the sample.	[optional]
sorted_from	str	Links to a larger sample from which this sample was obtained through sorting.	[optional]
sorted_from_detail	str	Detail for sample sorted into fractions capturing information about sorting.	[optional]
construct_library_sets	List[str]	The construct library sets of vectors introduced to this sample prior to performing an assay.	[optional]
moi	float	The actual multiplicity of infection (MOI) for vectors introduced to this sample. At least one construct library set must be specified in order to specify MOI. This property should capture the actual MOI, and not the targeted MOI.	[optional]
nucleic_acid_delivery	str	Method of introduction of nucleic acid into the cell.	[optional]
time_post_library_delivery	float	The time that elapsed past the time-point when the construct library sets were introduced.	[optional]
time_post_library_delivery_units	str	The units of time that elapsed past the point when the construct library sets were introduced.	[optional]
classifications	List[str]	The general category of this type of sample.	[optional]
time_post_change	float	The time that elapsed past the time-point when the cell fate change treatments were introduced.	[optional]
time_post_change_units	str	The units of time that elapsed past the point when the cell fate change treatments were introduced.	[optional]
cell_fate_change_treatments	List[str]	A list of treatments applied to the biosample with the purpose of differentiation, dedifferentiation, or reprogramming.	[optional]
cell_fate_change_protocol	str	A protocol applied to the biosample with the purpose of differentiation, dedifferentiation, or reprogramming.	[optional]
demultiplexed_from	str	The biosample this in vitro system sample was demultiplexed from using computational methods.	[optional]
passage_number	int	Number of passages including the passages from the source.	[optional]
targeted_sample_term	str	Ontology term identifying the targeted endpoint biosample resulting from differentation or reprogramming.	[optional]
growth_medium	str	A growth medium of the in vitro system.	[optional]
file_sets	List[str]	The file sets linked to this sample.	[optional]
multiplexed_in	List[str]	The multiplexed samples in which this sample is included.	[optional]
sorted_fractions	List[str]	The fractions into which this sample has been sorted.	[optional]
origin_of	List[str]	The samples which originate from this sample, such as through a process of cell differentiation.	[optional]
institutional_certificates	List[str]	The institutional certificates under which use of this sample is approved.	[optional]
upper_bound_age_in_hours	float	Upper bound of age of organism in hours at the time of collection of the sample.	[optional]
lower_bound_age_in_hours	float	Lower bound of age of organism in hours at the time of collection of the sample .	[optional]
parts	List[str]	The parts into which this sample has been divided.	[optional]
pooled_in	List[str]	The pooled samples in which this sample is included.	[optional]
demultiplexed_to	List[str]	The parts into which this sample has been demultiplexed.	[optional]
multiplexed_samples	List[str]	The samples multiplexed together to produce this sample.	[optional]
barcode_sample_map	str	The link to the barcode to sample mapping tabular file.	[optional]
sample_material	str		[optional]
pmi	int	The amount of time elapsed since death.	[optional]
pmi_units	str	The unit in which the PMI time was reported.	[optional]
ccf_id	str	HubMap Common Coordinate Framework unique identifier corresponding to the organ, biological structure, and spatial location of the tissue specimen.	[optional]
preservation_method	str	The method by which the tissue was preserved: cryopreservation (slow-freeze) or flash-freezing.	[optional]
used_by	List[str]	The component(s) of the IGVF consortium that utilize this software.	[optional]
versions	List[str]	A list of versions that have been released for this software.	[optional]
software	str	Unique name of the software package.	[optional]
version	str	The version of a particular software.	[optional]
download_id	str	The MD5 checksum, SHA-1 commit ID, image hash, or similar permanent identifier of the particular version of software used.	[optional]
downloaded_url	str	An external resource to track the version of the software downloaded.	[optional]
amount	float	Specific quantity of the applied treatment (used in conjunction with amount_units).	[optional]
amount_units	str	A unit for an amount other than those for time or temperature.	[optional]
duration	float	Duration indicates the time elapsed between the start and end of the treatment.	[optional]
duration_units	str	A unit of time.	[optional]
p_h	float	Final pH of the solution containing a chemical compound (if applicable)	[optional]
purpose	str	The intended purpose for treating the samples; Activation: treatment is known to activate a pathway in the biosample; Agonist: a substance which is known to initiate a physiological response when combined with a receptor; Antagonist: a substance that is known to interfere with or inhibits the physiological action of another; Control: treatment applied to a sample for control purposes; Differentiation: treatment that is applied to convert a less specialized cell to a more specialized cell; De-differentiation: treatment used to reprogram differentiated cells back to less determined cell states; Perturbation: treatment applied to the sample in order to study the effect of its application; Selection: treatment used to affect biosample in a way that can be used to distinguish cells and select for in the downstream steps; Stimulation: treatment applied to stimulate a cellular pathway.	[optional]
post_treatment_time	float	Post treatment time in conjunction with post treatment time units is used to specify the time that has passed between the point when biosamples were removed from the treatment solution before being sampled or treated with the next treatment.	[optional]
post_treatment_time_units	str	A unit of time.	[optional]
temperature	float	The temperature in Celsius to which the sample was exposed	[optional]
temperature_units	str	A unit of temperature.	[optional]
treatment_type	str	The classification of treatment agent that specifies its exact molecular nature. Chemical type refers to (natural or synthetic) organic/inorganic compounds and also includes drugs, while protein type is restricted to active protein biomolecules that are naturally or artifically synthesized via cellular translation mechanism of converting DNA into a protein. Environmental type referes to other external conditions that directly influence biological processes or reactions within a given environment. Example of chemical type: lactate, ethanol,hydrocortisone, LPS etc. Example of protein type: Interferons, interlukin, antibodies, etc. Example of chemical type: stiffness.	[optional]
treatment_term_id	str	Ontology identifier describing a component in the treatment.	[optional]
treatment_term_name	str	Ontology term describing a component in the treatment that is the principal component affecting the biosample being treated. Examples: interferon gamma, interleukin-4, Fibroblast growth factor 2, 20-hydroxyecdysone, 5-bromouridine etc.	[optional]
depletion	bool	Treatment is depleted.	[optional]
biosamples_treated	List[str]	The samples which have been treated using this treatment.	[optional]
email	str	The email associated with the user's account.	[optional]
first_name	str	The user's first (given) name.	[optional]
last_name	str	The user's last (family) name.	[optional]
submits_for	List[str]	Labs user is authorized to submit data for.	[optional]
groups	List[str]	Additional access control groups	[optional]
viewing_groups	List[str]	The group that determines which set of data the user has permission to view.	[optional]
job_title	str	The role of the user in their lab or organization.	[optional]
workflow_repositories	List[str]	Resources hosting the workflow.	[optional]
standards_page	str	A link to a page describing the standards for this workflow.	[optional]
workflow_version	int	The version of this workflow.	[optional]
analysis_steps	List[str]	The analysis steps which are part of this workflow.	[optional]

Example

from igvf_client.models.item import Item

# TODO update the JSON string below
json = "{}"
# create an instance of Item from a JSON string
item_instance = Item.from_json(json)
# print the JSON string representation of the object
print(Item.to_json())

# convert the object into a dict
item_dict = item_instance.to_dict()
# create an instance of Item from a dict
item_from_dict = Item.from_dict(item_dict)

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