is a Ontology.
The Common Coordinate Framework (CCF) Ontology is the spatial and semantic framework that underpins the Human Reference Atlas (HRA) developed within the NIH Human BioMolecular Atlas Program (HuBMAP). It encodes the relationships among anatomical structures, cell types, and biomarkers captured in the ASCT+B (Anatomical Structures, Cell Types, plus Biomarkers) tables, linking them to established ontologies such as Uberon, FMA, and Cell Ontology. The CCF also provides a spatial component that supports 3D spatial registration of tissue samples to reference organs via the CCF Registration User Interface, giving each sample a defined location in a common coordinate system. Together these clinical, semantic, and spatial layers serve as a primary upstream source for the HRA Knowledge Graph (HRA-KG).
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| ccf.owl | CCF Ontology (OWL) | ccf.owl (42.6 MB) | OntologyProduct | owl | The Common Coordinate Framework (CCF)... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| hra-kg.graph.ttl | HRA KG graph data, v2.2, Turtle format | graph.ttl (194.6 MB) | GraphProduct | ttl | had primary source | The graph representation of the Human... |
| hra-kg.graph.json | HRA KG graph data, v2.2, JSON-LD format | graph.json (17.6 KB) | GraphProduct | jsonld | had primary source | The graph representation of the Human... |
| hra-kg.graph.xml | HRA KG graph data, v2.2, RDF/XML format | graph.xml (176.5 MB) | GraphProduct | rdfxml | had primary source | The graph representation of the Human... |
| hra-kg.graph.nt | HRA KG graph data, v2.2, N-Triples format | graph.nt (277.9 MB) | GraphProduct | ntriples | had primary source | The graph representation of the Human... |
| hra-kg.graph.nq | HRA KG graph data, v2.2, N-Quads format | graph.nq (359.5 MB) | GraphProduct | nquads | had primary source | The graph representation of the Human... |
The Common Coordinate Framework (CCF) Ontology is the spatial and semantic backbone of the Human Reference Atlas (HRA), built within the NIH Human BioMolecular Atlas Program (HuBMAP). It brings together three complementary layers: a semantic layer that describes anatomical structures, cell types, and biomarkers via the ASCT+B tables (linked to Uberon, FMA, Cell Ontology, HGNC, and related ontologies); a spatial layer that places tissue blocks and organs in a shared 3D coordinate system; and clinical metadata about specimens and donors. Spatial registration of tissue samples to reference organs is performed through the CCF Registration User Interface.
As an upstream source for the HRA Knowledge Graph (HRA-KG), the CCF Ontology supplies the standardized terms and spatial relationships that allow cross-scale biological queries spanning whole organs down to individual cells.
https://cdn.humanatlas.io/digital-objects/graph/ccf/latest/assets/ccf.owl.Created: June 18, 2026 | Last modified: June 18, 2026