Imaged specimen

Gross imageimaged_specimen.overview_images (array) List of filenames of photographs of specimen. For example "my_image_file.jpg" or "overview_image.tiff".

Imaged slice thicknessRequiredimaged_specimen.slice_thickness (number) Thickness of the imaged slice in micrometres. For example "14".

Imaged specimen>Internal tissue structures (organ_part_ontology array) Internal (landmark) structures visible in the overview image that are informative about the broader anatomical context/location of the sample.

Organ part ontology IDimaged_specimen.internal_anatomical_structures.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 labelimaged_specimen.internal_anatomical_structures.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 partRequiredimaged_specimen.internal_anatomical_structures.text (string from organ_part_ontology) The text for the term as the user provides it. For example "bone marrow" or "islet of Langerhans".

Imaged specimen>Biomaterial coreRequired (biomaterial_core object) Core biomaterial-level information.

HDBR accessionimaged_specimen.biomaterial_core.HDBR_accession (string from biomaterial_core) A Human Developmental Biology Resource (HDBR) sample accession. For example "34526" or "14758, 2, liver".

Biomaterial descriptionimaged_specimen.biomaterial_core.biomaterial_description (string from biomaterial_core) A general description of the biomaterial.

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

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

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

Genotypeimaged_specimen.biomaterial_core.genotype (string from biomaterial_core) Genotype of the biomaterial. For example "DRB1 0401 protective allele" or "HLA-B*3901 allele".

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

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

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

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

Timecourse relevanceimaged_specimen.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 valueRequiredimaged_specimen.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".

Imaged specimen>Biomaterial core>Timecourse>Timecourse unitRequired (time_unit_ontology object) The unit in which the Timecourse value is expressed.

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

Imaged specimen>provenance (provenance object) Provenance information provided by the system.

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

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

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

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

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

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

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

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