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Metadata

Organoid

Information about an organoid biomaterial.

View JSON source: organoiddoneShow required fields only

Properties

Organoid ageorganoid.agecopy (number) Age of the organoid in Organoid age unit measured from when cell aggregates started differentiating to desired organoid model. For example "55".
Embeddded in matrigelorganoid.embedded_in_matrigelcopy (boolean) Whether the organoid is embedded in a matrigel. For example "Should be one of: yes, no.".
Growth environmentorganoid.growth_environmentcopy (string) Growth environment in which the organoid is grown. For example "matrigel", "liquid suspension" or "adherent".
Input aggregate cell countorganoid.input_aggregate_cell_countcopy (number) Estimated number of cells per input cell aggregate. For example "10000".
Organoid morphologyorganoid.morphologycopy (string) General description of the organoid morphology. For example "Epithelial monolayer with budding crypt-like domains" or "Optic cup structure".
Organoid sizeorganoid.sizecopy (number) Size of the organoid in Organoid size unit. For example "4".
Stored oxygen levelorganoid.stored_oxygen_levelscopy (number) Percent oxygen level organoid was stored in prior to sequencing. For example "75".
Organoid>Organoid age unit (time_unit_ontology object) The unit in which Organoid age is expressed.
Time unit ontology IDorganoid.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 labelorganoid.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 unitRequiredorganoid.age_unit.textcopy (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".
Organoid>Genus species (species_ontology array) The scientific binomial name for the species of the organoid.
Species ontology IDorganoid.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 labelorganoid.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".
SpeciesRequiredorganoid.genus_species.textcopy (string from species_ontology) The name of the species to which the organism belongs. For example "Homo sapiens" or "Mus musculus".
Organoid>Organ modelRequired (organ_ontology object) Organ for which this organoid is a model system.
Organ ontology IDorganoid.model_organ.ontologycopy (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 labelorganoid.model_organ.ontology_labelcopy (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".
OrganRequiredorganoid.model_organ.textcopy (string from organ_ontology) The text for the term as the user provides it. For example "heart" or "immune system".
Organoid>Organ part model (organ_part_ontology object) Organ part for which this organoid is a model system.
Organ part ontology IDorganoid.model_organ_part.ontologycopy (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 labelorganoid.model_organ_part.ontology_labelcopy (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 partRequiredorganoid.model_organ_part.textcopy (string from organ_part_ontology) The text for the term as the user provides it. For example "bone marrow" or "islet of Langerhans".
Organoid>Organoid size unit (length_unit_ontology object) The unit in which the Organoid size is expressed.
Length unit ontology IDorganoid.size_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 labelorganoid.size_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 unitRequiredorganoid.size_unit.textcopy (string from length_unit_ontology) The name of a length unit being used. For example "micrometer" or "meter".
Organoid>Biomaterial coreRequired (biomaterial_core object) Core biomaterial-level information.
HDBR accessionorganoid.biomaterial_core.HDBR_accessioncopy (string from biomaterial_core) A Human Developmental Biology Resource (HDBR) sample accession. For example "34526" or "14758, 2, liver".
Biomaterial descriptionorganoid.biomaterial_core.biomaterial_descriptioncopy (string from biomaterial_core) A general description of the biomaterial.
Biomaterial IDRequiredorganoid.biomaterial_core.biomaterial_idcopy (string from biomaterial_core) A unique ID for the biomaterial.
Biomaterial nameorganoid.biomaterial_core.biomaterial_namecopy (string from biomaterial_core) A short, descriptive name for the biomaterial that need not be unique.
BioSamples accessionorganoid.biomaterial_core.biosamples_accessioncopy (string from biomaterial_core) A BioSamples accession. For example "SAMN00000000".
Genotypeorganoid.biomaterial_core.genotypecopy (string from biomaterial_core) Genotype of the biomaterial. For example "DRB1 0401 protective allele" or "HLA-B*3901 allele".
INSDC sample accessionorganoid.biomaterial_core.insdc_sample_accessioncopy (string from biomaterial_core) An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. For example "SRS0000000".
NCBI taxon IDRequiredorganoid.biomaterial_core.ncbi_taxon_idcopy (array from biomaterial_core) A taxonomy ID (taxonID) from NCBI. For example "9606".
Supplementary filesorganoid.biomaterial_core.supplementary_filescopy (array from biomaterial_core) A list of filenames of biomaterial-level supplementary files. For example "sample_site_image.jpg".
Organoid>provenance (provenance object) Provenance information provided by the system.
Accessionorganoid.provenance.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredorganoid.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versionorganoid.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versionorganoid.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredorganoid.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDorganoid.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update dateorganoid.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDorganoid.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.