HCA Data Portal

Imaged specimen

Information about a tissue specimen after it has been sectioned and prepared for imaging.

View JSON source: imaged_specimendoneShow required fields only


Gross imageimaged_specimen.overview_imagescopy (array) List of filenames of photographs of specimen. For example "my_image_file.jpg" or "overview_image.tiff".
Imaged slice thicknessRequiredimaged_specimen.slice_thicknesscopy (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.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 labelimaged_specimen.internal_anatomical_structures.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 partRequiredimaged_specimen.internal_anatomical_structures.textcopy (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_accessioncopy (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_descriptioncopy (string from biomaterial_core) A general description of the biomaterial.
Biomaterial IDRequiredimaged_specimen.biomaterial_core.biomaterial_idcopy (string from biomaterial_core) A unique ID for the biomaterial.
Biomaterial nameimaged_specimen.biomaterial_core.biomaterial_namecopy (string from biomaterial_core) A short, descriptive name for the biomaterial that need not be unique.
BioSamples accessionimaged_specimen.biomaterial_core.biosamples_accessioncopy (string from biomaterial_core) A BioSamples accession. For example "SAMN00000000".
Genotypeimaged_specimen.biomaterial_core.genotypecopy (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_accessioncopy (string from biomaterial_core) An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. For example "SRS0000000".
NCBI taxon IDRequiredimaged_specimen.biomaterial_core.ncbi_taxon_idcopy (array from biomaterial_core) A taxonomy ID (taxonID) from NCBI. For example "9606".
Supplementary filesimaged_specimen.biomaterial_core.supplementary_filescopy (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.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 valueRequiredimaged_specimen.biomaterial_core.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".
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.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 labelimaged_specimen.biomaterial_core.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 unitRequiredimaged_specimen.biomaterial_core.timecourse.unit.textcopy (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.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredimaged_specimen.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versionimaged_specimen.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versionimaged_specimen.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredimaged_specimen.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDimaged_specimen.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update dateimaged_specimen.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDimaged_specimen.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.