Specimen from organism

Time of collectionspecimen_from_organism.collection_time (string) When the biomaterial was collected. For example "2016-01-21T00:00:00Z" or "2016-03".

Transplant organspecimen_from_organism.transplant_organ (boolean) Was the specimen collected after extraction for organ transplantation? For example "yes" or "no".

Specimen from organism>Adjacent disease(s) (disease_ontology array) Short description of the disease(s) adjacent to the specimen's collection site (e.g. breast cancer).

Disease ontology IDspecimen_from_organism.adjacent_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 labelspecimen_from_organism.adjacent_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".

DiseaseRequiredspecimen_from_organism.adjacent_diseases.text (string from disease_ontology) The text for the term as the user provides it. For example "type 2 diabetes mellitus" or "normal".

Specimen from organism>Known disease(s) (disease_ontology array) Short description of known disease(s) of the specimen.

Disease ontology IDspecimen_from_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 labelspecimen_from_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".

DiseaseRequiredspecimen_from_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".

Specimen from organism>Genus species (species_ontology array) The scientific binomial name for the species of the specimen.

Species ontology IDspecimen_from_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 labelspecimen_from_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".

SpeciesRequiredspecimen_from_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".

Specimen from organism>OrganRequired (organ_ontology object) The organ that the biomaterial came from.

Organ ontology IDspecimen_from_organism.organ.ontology (string from organ_ontology) An ontology term identifier in the form prefix:accession. For example "UBERON:0000948" or "UBERON:0002405".Graph restriction: Subclasses of UBERON:0000465 from obo:hcao or obo:uberon including self.

Organ ontology labelspecimen_from_organism.organ.ontology_label (string from organ_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 "heart" or "immune system".

OrganRequiredspecimen_from_organism.organ.text (string from organ_ontology) The text for the term as the user provides it. For example "heart" or "immune system".

Specimen from organism>Organ part (organ_part_ontology array) A term for a specific part of the organ that the biomaterial came from.

Organ part ontology IDspecimen_from_organism.organ_parts.ontology (string from organ_part_ontology) An ontology term identifier in the form prefix:accession. For example "UBERON:0002371" or "UBERON:0000006".Graph restriction: Subclasses of UBERON:0000465 from obo:hcao or obo:uberon including self.

Organ part ontology labelspecimen_from_organism.organ_parts.ontology_label (string from organ_part_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 "bone marrow" or "islet of Langerhans".

Organ partRequiredspecimen_from_organism.organ_parts.text (string from organ_part_ontology) The text for the term as the user provides it. For example "bone marrow" or "islet of Langerhans".

Specimen from organism>Preservation/Storage (preservation_storage object) Information about how a specimen was preserved and/or stored over a period of time.

Preservation methodspecimen_from_organism.preservation_storage.preservation_method (string enum from preservation_storage) The method by which a biomaterial was preserved through the use of chemicals, cold, or other means to prevent or retard biological or physical deterioration. Should be one of: "cryopreservation in liquid nitrogen (dead tissue)", "cryopreservation in dry ice (dead tissue)", "cryopreservation of live cells in liquid nitrogen", "cryopreservation, other", "formalin fixed, unbuffered", "formalin fixed, buffered", "formalin fixed and paraffin embedded", "hypothermic preservation media at 2-8C" or "fresh".

Storage methodspecimen_from_organism.preservation_storage.storage_method (string enum from preservation_storage) The method by which a biomaterial was stored after preservation or before another protocol was used. Should be one of: "ambient temperature", "cut slide", "fresh", "frozen at -70C", "frozen at -80C", "frozen at -150C", "frozen in liquid nitrogen", "frozen in vapor phase", "paraffin block", "RNAlater at 4C", "RNAlater at 25C" or "RNAlater at -20C".

Storage timespecimen_from_organism.preservation_storage.storage_time (number from preservation_storage) Length of time the biomaterial was stored for in Storage time units. For example "5".

Specimen from organism>Preservation/Storage>Storage time unit (time_unit_ontology object) The unit in which Storage time is expressed.

Time unit ontology IDspecimen_from_organism.preservation_storage.storage_time_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 labelspecimen_from_organism.preservation_storage.storage_time_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 unitRequiredspecimen_from_organism.preservation_storage.storage_time_unit.text (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".

Specimen from organism>Purchased specimen (purchased_reagents object) Information about a purchased specimen.

Catalog numberspecimen_from_organism.purchased_specimen.catalog_number (string from purchased_reagents) The catalog number of the kit/reagent. For example "20014279".

Expiry datespecimen_from_organism.purchased_specimen.expiry_date (string from purchased_reagents) The date of expiration for the kit/reagent. For example "2018-01-31" or "2018-01".

Titerspecimen_from_organism.purchased_specimen.kit_titer (string from purchased_reagents) Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. For example "3.0x10^7".

Batch/lot numberspecimen_from_organism.purchased_specimen.lot_number (string from purchased_reagents) The batch or lot number of the kit/reagent. For example "10001A".

Manufacturerspecimen_from_organism.purchased_specimen.manufacturer (string from purchased_reagents) The manufacturer of the kit/reagent. For example "Illumina" or "ThermoFisher Scientific".

Retail namespecimen_from_organism.purchased_specimen.retail_name (string from purchased_reagents) The retail name of the kit/reagent. For example "SureCell WTA 3' Library Prep Kit" or "CytoTune iPS 2.0 Sendai Reprogramming Kit".

Specimen from organism>State of specimen (state_of_specimen object) State of the specimen at the time of collection.

Autolysis scorespecimen_from_organism.state_of_specimen.autolysis_score (string enum from state_of_specimen) State of tissue breakdown due to self-digestion. Should be one of: "none", "mild" or "moderate".

Gross descriptionspecimen_from_organism.state_of_specimen.gross_description (string from state_of_specimen) Color, size, and other aspects of specimen as visible to naked eye. For example "focal wedge shaped region of tan-orange discoloration" or "cystic".

Gross imagespecimen_from_organism.state_of_specimen.gross_images (array from state_of_specimen) List of filenames of photographs of specimen without magnification. For example "my_gross_image_file.jpg".

Ischemic temperaturespecimen_from_organism.state_of_specimen.ischemic_temperature (string enum from state_of_specimen) Whether specimen experienced warm or cold ischemia. Should be one of: "warm" or "cold".

Ischemic timespecimen_from_organism.state_of_specimen.ischemic_time (integer from state_of_specimen) Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. For example "7200".

Microscopic descriptionspecimen_from_organism.state_of_specimen.microscopic_description (string from state_of_specimen) How the specimen looks under the microscope and how it compares with normal cells. For example "Mixture of different cell sizes apparent" or "Dead cells are quite faint on microscope".

Microscopic imagespecimen_from_organism.state_of_specimen.microscopic_images (array from state_of_specimen) List of filenames of photographs of specimen under microscope. For example "my_microscopic_image_file.jpg".

Post-mortem intervalspecimen_from_organism.state_of_specimen.postmortem_interval (integer from state_of_specimen) Duration of time between when death was declared and when the specimen was preserved or processed. For example "2400".

Specimen from organism>Biomaterial coreRequired (biomaterial_core object) Core biomaterial-level information.

HDBR accessionspecimen_from_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 descriptionspecimen_from_organism.biomaterial_core.biomaterial_description (string from biomaterial_core) A general description of the biomaterial.

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

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

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

Genotypespecimen_from_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 accessionspecimen_from_organism.biomaterial_core.insdc_sample_accession (string from biomaterial_core) An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. For example "SRS0000000".

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

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

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

Timecourse relevancespecimen_from_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 valueRequiredspecimen_from_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".

Specimen from organism>Biomaterial core>Timecourse>Timecourse unitRequired (time_unit_ontology object) The unit in which the Timecourse value is expressed.

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

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

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

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

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

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

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

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

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

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