Donor organism

Gestational agedonor_organism.gestational_age (string) Gestational age of pregnancy in Gestational age units measured from the last menstrual period. For example "22" or "8-9".

Heightdonor_organism.height (string) Height of organism in Height unit. For example "160" or "120-140".

Alive at collectionRequireddonor_organism.is_living (string enum) Whether organism was alive at time of biomaterial collection. Should be one of: "yes", "no", "unknown" or "not applicable".

Agedonor_organism.organism_age (string) Age of organism in Age units measured since birth. For example "20" or "45-65".

Biological sexRequireddonor_organism.sex (string enum) The biological sex of the organism. Should be one of: "female", "male", "mixed" or "unknown".

Weightdonor_organism.weight (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_death (string from death) Conditions resulting in death. For example "Hypoxic brain damage" or "Sudden cardiac arrest".

Cold perfuseddonor_organism.death.cold_perfused (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_ventilator (number from death) Number of days on ventilator before death occurred. For example "4".

Value on Hardy scaledonor_organism.death.hardy_scale (integer from death) Value on 4-point Hardy scale cause of death classification. For example "0".

Normothermic regional perfusiondonor_organism.death.normothermic_regional_perfusion (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_type (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_death (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.ontology (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_label (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.text (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.ontology (string from disease_ontology) An ontology term identifier in the form prefix:accession. For example "MONDO:0005148", "PATO:0000461" or "HP:0001397".Graph restriction: Subclasses of MONDO:0000001, PATO:0000461, HP:0000118 from obo:mondo or obo:efo or obo:hp including self.

Disease ontology labeldonor_organism.diseases.ontology_label (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.text (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.child (string from familial_relationship) The individual's child.

Parentdonor_organism.familial_relationships.parent (string from familial_relationship) The individual's parent.

Siblingdonor_organism.familial_relationships.sibling (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.ontology (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_label (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.text (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.ontology (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_label (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.text (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.ontology (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_label (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.text (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_index (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.ontology (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_label (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.text (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_history (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.medication (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_state (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_history (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_results (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.treatment (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.ontology (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_label (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.text (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.ontology (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_label (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.text (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.ontology (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_label (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.text (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_accession (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_description (string from biomaterial_core) A general description of the biomaterial.

Biomaterial IDRequireddonor_organism.biomaterial_core.biomaterial_id (string from biomaterial_core) A unique ID for the biomaterial.

Biomaterial namedonor_organism.biomaterial_core.biomaterial_name (string from biomaterial_core) A short, descriptive name for the biomaterial that need not be unique.

BioSamples accessiondonor_organism.biomaterial_core.biosamples_accession (string from biomaterial_core) A BioSamples accession. For example "SAMN00000000".

Genotypedonor_organism.biomaterial_core.genotype (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_accession (string from biomaterial_core) An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. For example "SRS0000000".

NCBI taxon IDRequireddonor_organism.biomaterial_core.ncbi_taxon_id (array from biomaterial_core) A taxonomy ID (taxonID) from NCBI. For example "9606".

Supplementary filesdonor_organism.biomaterial_core.supplementary_files (array from biomaterial_core) A list of filenames of biomaterial-level supplementary files. For example "sample_site_image.jpg".

Donor organism>Biomaterial core>Timecourse (timecourse object) Information relating to a timecourse associated with this biomaterial.

Timecourse relevancedonor_organism.biomaterial_core.timecourse.relevance (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.biomaterial_core.timecourse.value (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>Biomaterial core>Timecourse>Timecourse unitRequired (time_unit_ontology object) The unit in which the Timecourse value is expressed.

Time unit ontology IDdonor_organism.biomaterial_core.timecourse.unit.ontology (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.biomaterial_core.timecourse.unit.ontology_label (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.biomaterial_core.timecourse.unit.text (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".

Donor organism>provenance (provenance object) Provenance information provided by the system.

Accessiondonor_organism.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequireddonor_organism.provenance.document_id (string from provenance) Identifier for document.

Schema major versiondonor_organism.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versiondonor_organism.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequireddonor_organism.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDdonor_organism.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update datedonor_organism.provenance.update_date (string from provenance) When project was last updated.

Updater IDdonor_organism.provenance.updater_id (string from provenance) ID of individual who last updated project.