Ontologies
The HCA metadata team uses a dedicated application Ontology - the HCA Ontology or HCAO.
Which Ontologies
| Field type | Ontology | Example fields |
|---|---|---|
| Anatomical location | Uber-anatomy ontology (UBERON) | specimen_from_organism.organ specimen_from_organism.organ_parts |
| Cell types | Cell ontology (CL) | cell_suspension.selected_cell_types |
| Experimental factors | Experimental Factor Ontology (EFO) | dissociation_protocol.method library_preparation_protocol.library_construction_method |
| Ethnicity | Human Ancestry Ontology (HANCESTRO) | donor_organism.ethnicity |
| Units | Units of measurement Ontology (UO) | donor_organism.age_unit |
| Species | NCBI organismal classification (NCBITaxon) | donor_organism.biomaterial_core.genus_species |
| Developmental stage (human) | Human Developmental Stages (HSAPDV) | donor_organism.development_stage |
| Developmental stage (mouse) | Experimental Factor Ontology (EFO) | donor_organism.development_stage |
| Diseases | Mondo Disease Ontology (MONDO) | donor_organism.diseases |
| File content | Bioinformatics operations, data types, formats, identifiers and topics (EDAM) | sequence_file.file_core.content_description |
| Chemicals & Molecules | Chemical Entities of Biological Interest (CHEBI) | library_preparation_protocol.input_nucleic_acid_molecule |
| Imaging techniques | Biological Imaging Methods Ontology (FBBI) | imaging_protocol.microscopy_technique |