Cell Ontology

The Cell Ontology (CL) is our flagship product: a dynamic, structured vocabulary of cell types that has become the community standard for annotating single-cell and spatial data. It provides precise, logically defined, cross-species cell type classes that make cell annotations comparable, searchable, and interpretable — turning cell type labels into a gateway to the wider biological knowledge about each cell type.

CL is used to annotate data across major resources including CELLxGENE, the Human Cell Atlas, and the Ontology Lookup Service, and is a founding ontology of the OBO Foundry.

Explore: GitHub · Ontology Lookup Service · Tan et al. (2026), The Cell Ontology in the age of single-cell omics

Aims#

We are extending the Cell Ontology to keep pace with the explosion of single-cell and spatial reference data, and to make it the connective tissue between atlases.

Incorporating transcriptomic reference data#

Adding terms — and links from CL classes to the cell types defined in transcriptomic reference atlases — from:

• BICAN — the BRAIN Initiative Cell Atlas Network.
• HCA v1 atlases — the Human Cell Atlas first-generation reference atlases.
• Pan-tissue Azimuth (PAZ) — cross-tissue reference cell types.
• HuBMAP Human Reference Atlas (HRA) — anatomy- and cell-type reference for the healthy human body.

Linking cell types to reference data#

Building explicit links from Cell Ontology terms to the transcriptomically defined cell types in these atlases — so that a CL term connects users directly to the reference data, markers and evidence that define it.

Related work#

• Single Cell Knowledge Graph — surfaces markers and evidence, and highlights gaps in CL that new data can fill.
• Standards & tools — the Cell Annotation Schema and tools for capturing the evidence behind CL annotations.