The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.

Prefix

ccf

Keywords

ontology

Version

2.3.0

License

CC-BY-4.0

Links

Homepage Repository OWL Request Discussion

Contact

Katy Börner   0000-0002-3321-6137   katyb

Pattern for Local Unique Identifiers

Local identifiers in Human Reference Atlas Common Coordinate Framework Ontology should match this regular expression:
^\S+$

Example Local Unique Identifier

extraction_set   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Human Reference Atlas Common Coordinate Framework Ontology should match this regular expression:
^ccf:\S+$

Example CURIE

ccf:extraction_set

Contributors

• submitter Benjamin M. Gyori   0000-0001-9439-5346   bgyori

Reviewer

Charles Tapley Hoyt   0000-0003-4423-4370   cthoyt

The metaregistry provides mappings between the Bioregistry and other registries. There are 4 mappings to external registries for this resource with 2 unique external prefixes.

When using this resource in RDF, the following URI format should be used:

http://purl.org/ccf/$1

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier extraction_set is used to demonstrate the providers available for Human Reference Atlas Common Coordinate Framework Ontology. A guide for curating additional providers can be found here.