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Donor organism

Information about the donor from which a specimen was collected.

View JSON source: donor_organismdoneShow required fields only

Properties

Gestational agedonor_organism.gestational_agecopy (string) Gestational age of pregnancy in Gesational age units measured from the last menstrual period. For example "22" or "8-9".
Heightdonor_organism.heightcopy (string) Height of organism in Height unit. For example "160" or "120-140".
Alive at collectionRequireddonor_organism.is_livingcopy (string enum) Whether organism was alive at time of biomaterial collection. Should be one of: "yes", "no", "unknown" or "not applicable".
Agedonor_organism.organism_agecopy (string) Age of organism in Age units measured since birth. For example "20" or "45-65".
Biological sexRequireddonor_organism.sexcopy (string enum) The biological sex of the organism. Should be one of: "female", "male", "mixed" or "unknown".
Weightdonor_organism.weightcopy (string) Weight of organism in Weight unit. For example "60" or "40-60".
Donor organism>Death conditions (death object) Information about conditions of death of the organism.
Cause of deathRequireddonor_organism.death.cause_of_deathcopy (string from death) Conditions resulting in death. For example "Hypoxic brain damage" or "Sudden cardiac arrest".
Cold perfuseddonor_organism.death.cold_perfusedcopy (boolean from death) Whether perfusion with cold fluid was used to help preserve tissues before heart stopped. For example "Should be one of: yes, no.".
Number of days on ventilatordonor_organism.death.days_on_ventilatorcopy (number from death) Number of days on ventilator before death occurred. For example "4".
Value on Hardy scaledonor_organism.death.hardy_scalecopy (integer from death) Value on 4-point Hardy scale cause of death classification. For example "0".
Normothermic regional perfusiondonor_organism.death.normothermic_regional_perfusioncopy (string enum from death) Whether entire body was perfused with warm oxygenated blood. Should be one of: "yes", "no" or "unknown".
Organ donation death typedonor_organism.death.organ_donation_death_typecopy (string enum from death) Type of death preceding organ donation. Should be one of: "Donation after circulatory death (DCD)" or "Donation after brainstem death (DBD)".
Time of deathdonor_organism.death.time_of_deathcopy (string from death) Date and time when death was declared. For example "2016-01-21T00:00:00Z" or "2016-03".
Donor organism>Development stageRequired (development_stage_ontology object) A classification of the developmental stage of the organism.
Development stage ontology IDdonor_organism.development_stage.ontologycopy (string from development_stage_ontology) An ontology term identifier in the form prefix:accession. For example "HsapDv:0000087" or "EFO:0002588".Graph restriction: Subclasses of EFO:0000399, HsapDv:0000000, UBERON:0000105 from obo:efo or obo:hcao.
Development stage ontology labeldonor_organism.development_stage.ontology_labelcopy (string from development_stage_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "human adult stage" or "Theiler stage 28".
Development stageRequireddonor_organism.development_stage.textcopy (string from development_stage_ontology) The name of the development stage of the organism. For example "human adult stage" or "Theiler stage 28".
Donor organism>Known disease(s) (disease_ontology array) Short description of known disease(s) of the organism.
Disease ontology IDdonor_organism.diseases.ontologycopy (string from disease_ontology) An ontology term identifier in the form prefix:accession. For example "MONDO:0005148" or "PATO:0000461".Graph restriction: Subclasses of MONDO:0000001, PATO:0000461 from obo:mondo or obo:efo including self.
Disease ontology labeldonor_organism.diseases.ontology_labelcopy (string from disease_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "type 2 diabetes mellitus" or "normal".
DiseaseRequireddonor_organism.diseases.textcopy (string from disease_ontology) The text for the term as the user provides it. For example "type 2 diabetes mellitus" or "normal".
Donor organism>Familial relationship (familial_relationship array) Information about other organisms related to this organism.
Childdonor_organism.familial_relationships.childcopy (string from familial_relationship) The individual's child.
Parentdonor_organism.familial_relationships.parentcopy (string from familial_relationship) The individual's parent.
Siblingdonor_organism.familial_relationships.siblingcopy (string from familial_relationship) The individual's sibling.
Donor organism>Genus species (species_ontology array) The scientific binomial name for the species of the organism.
Species ontology IDdonor_organism.genus_species.ontologycopy (string from species_ontology) An ontology term identifier in the form prefix:accession. For example "NCBITaxon:9606" or "NCBITaxon:10090".Graph restriction: Subclasses of OBI:0100026, NCBITaxon:2759 from obo:efo or obo:NCBITaxon.
Species ontology labeldonor_organism.genus_species.ontology_labelcopy (string from species_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "Homo sapiens" or "Mus musculus".
SpeciesRequireddonor_organism.genus_species.textcopy (string from species_ontology) The name of the species to which the organism belongs. For example "Homo sapiens" or "Mus musculus".
Donor organism>Gestational age unit (time_unit_ontology object) The unit in which Gestational age is expressed.
Time unit ontology IDdonor_organism.gestational_age_unit.ontologycopy (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.
Time unit ontology labeldonor_organism.gestational_age_unit.ontology_labelcopy (string from time_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "second" or "week".
Time unitRequireddonor_organism.gestational_age_unit.textcopy (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".
Donor organism>Height unit (length_unit_ontology object) The unit in which Height is expressed.
Length unit ontology IDdonor_organism.height_unit.ontologycopy (string from length_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000017" or "UO:0000008".Graph restriction: Subclasses of UO:0000001 from obo:efo or obo:uo.
Length unit ontology labeldonor_organism.height_unit.ontology_labelcopy (string from length_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "micrometer" or "meter".
Length unitRequireddonor_organism.height_unit.textcopy (string from length_unit_ontology) The name of a length unit being used. For example "micrometer" or "meter".
Donor organism>Human-specific (human_specific object) Fields specific to human (homo sapiens) organisms.
Body mass indexdonor_organism.human_specific.body_mass_indexcopy (number from human_specific) The body mass index of the donor. For example "36.4".
Donor organism>Human-specific>Ethnicity (ethnicity_ontology array) Ethnicity of the donor.
Ethnicity ontology IDdonor_organism.human_specific.ethnicity.ontologycopy (string from ethnicity_ontology) An ontology term identifier in the form prefix:accession. For example "HANCESTRO:0005" or "HANCESTRO:0014".Graph restriction: Subclasses of HANCESTRO:0004 from obo:hancestro.
Ethnicity ontology labeldonor_organism.human_specific.ethnicity.ontology_labelcopy (string from ethnicity_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "European" or "Hispanic or Latin American".
EthnicityRequireddonor_organism.human_specific.ethnicity.textcopy (string from ethnicity_ontology) The ethnicity of the human donor. For example "European" or "Hispanic or Latin American".
Donor organism>Medical history (medical_history object) Information about the medical history of the organism.
Alcohol historydonor_organism.medical_history.alcohol_historycopy (string from medical_history) Estimated amount of alcohol consumed per day. For example "3-6 alcohol units/day" or "1 drink per day".
Medicationsdonor_organism.medical_history.medicationcopy (string from medical_history) Medications the individual was taking at time of biomaterial collection. For example "Naproxen 500mg/day" or "Citalopram 20mg/day".
Nutritional statedonor_organism.medical_history.nutritional_statecopy (string enum from medical_history) Nutritional state of individual at time of biomaterial collection. Should be one of: "normal", "fasting" or "feeding tube removed".
Smoking historydonor_organism.medical_history.smoking_historycopy (string from medical_history) Estimated number of cigarettes smoked per day. For example "20 cigarettes/day for 25 years, stopped 2000".
Test resultsdonor_organism.medical_history.test_resultscopy (string from medical_history) Results from medical tests performed on the individual. For example "lipid panel shows normal level of LDL (124 mg/dL)" or "HIV, HBV, HCV: Negative".
Treatmentsdonor_organism.medical_history.treatmentcopy (string from medical_history) Treatments the individual has undergone prior to biomaterial collection. For example "Patient treated with antibiotics for a urinary tract infection" or "Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer".
Donor organism>Mouse-specific (mouse_specific object) Fields specific to mouse (mus musculus) organisms.
Donor organism>Mouse-specific>Mouse strain (strain_ontology array) The name of the mouse strain.
Strain ontology IDdonor_organism.mouse_specific.strain.ontologycopy (string from strain_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0004472" or "EFO:0000602".Graph restriction: Subclasses of NCBITaxon:10090 from obo:efo or obo:NCBITaxon including self.
Strain ontology labeldonor_organism.mouse_specific.strain.ontology_labelcopy (string from strain_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "C57BL/6" or "BALB/c".
StrainRequireddonor_organism.mouse_specific.strain.textcopy (string from strain_ontology) The name of the strain to which the organism belongs. For example "C57BL/6" or "BALB/c".
Donor organism>Age unit (time_unit_ontology object) The unit in which Age is expressed.
Time unit ontology IDdonor_organism.organism_age_unit.ontologycopy (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.
Time unit ontology labeldonor_organism.organism_age_unit.ontology_labelcopy (string from time_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "second" or "week".
Time unitRequireddonor_organism.organism_age_unit.textcopy (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".
Donor organism>Timecourse (timecourse object) Information relating to a timecourse associated with this biomaterial.
Timecourse relevancedonor_organism.timecourse.relevancecopy (string from timecourse) Relevance of the Timecourse value/unit to the experiment. For example "Collection after tumor cells injected into the mammary gland" or "Time tissue underwent liberase digestion".
Timecourse valueRequireddonor_organism.timecourse.valuecopy (string from timecourse) The numerical value in Timecourse unit associated with a time interval used in the experiment. For example "2" or "5.5-10.5".
Donor organism>Timecourse>Timecourse unitRequired (time_unit_ontology object) The unit in which the Timecourse value is expressed.
Time unit ontology IDdonor_organism.timecourse.unit.ontologycopy (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.
Time unit ontology labeldonor_organism.timecourse.unit.ontology_labelcopy (string from time_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "second" or "week".
Time unitRequireddonor_organism.timecourse.unit.textcopy (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".
Donor organism>Weight unit (mass_unit_ontology object) The unit in which Weight is expressed.
Mass unit ontology IDdonor_organism.weight_unit.ontologycopy (string from mass_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000009" or "UO:0000023".Graph restriction: Subclasses of UO:0000002 from obo:efo or obo:uo.
Mass unit ontology labeldonor_organism.weight_unit.ontology_labelcopy (string from mass_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "kilogram" or "microgram".
Mass unitRequireddonor_organism.weight_unit.textcopy (string from mass_unit_ontology) The name of a mass unit being used. For example "kilogram" or "microgram".
Donor organism>Biomaterial coreRequired (biomaterial_core object) Core biomaterial-level information.
HDBR accessiondonor_organism.biomaterial_core.HDBR_accessioncopy (string from biomaterial_core) A Human Developmental Biology Resource (HDBR) sample accession. For example "34526" or "14758, 2, liver".
Biomaterial descriptiondonor_organism.biomaterial_core.biomaterial_descriptioncopy (string from biomaterial_core) A general description of the biomaterial.
Biomaterial IDRequireddonor_organism.biomaterial_core.biomaterial_idcopy (string from biomaterial_core) A unique ID for the biomaterial.
Biomaterial namedonor_organism.biomaterial_core.biomaterial_namecopy (string from biomaterial_core) A short, descriptive name for the biomaterial that need not be unique.
BioSamples accessiondonor_organism.biomaterial_core.biosamples_accessioncopy (string from biomaterial_core) A BioSamples accession. For example "SAMN00000000".
Genotypedonor_organism.biomaterial_core.genotypecopy (string from biomaterial_core) Genotype of the biomaterial. For example "DRB1 0401 protective allele" or "HLA-B*3901 allele".
INSDC sample accessiondonor_organism.biomaterial_core.insdc_sample_accessioncopy (string from biomaterial_core) An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. For example "SRS0000000".
NCBI taxon IDRequireddonor_organism.biomaterial_core.ncbi_taxon_idcopy (array from biomaterial_core) A taxonomy ID (taxonID) from NCBI. For example "9606".
Supplementary filesdonor_organism.biomaterial_core.supplementary_filescopy (array from biomaterial_core) A list of filenames of biomaterial-level supplementary files. For example "sample_site_image.jpg".
Donor organism>provenance (provenance object) Provenance information provided by the system.
Accessiondonor_organism.provenance.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequireddonor_organism.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versiondonor_organism.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versiondonor_organism.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequireddonor_organism.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDdonor_organism.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update datedonor_organism.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDdonor_organism.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.