Projects & Products

Part of the Wellcome Sanger Institute’s Cellular Genetics Programme, the Cellular Semantics team is dedicated to advancing knowledge in cell classification and understanding cellular diversity. We combine expertise in cell biology, bioinformatics, ontology development and agentic AI to help biologists — and biological databases — agree on what cell types are, describe them consistently, and connect them to the data and evidence behind them.

Our work spans open community standards, data-driven taxonomies, and a growing suite of AI-driven tools.

Ontologies#

• Cell Ontology (CL) — our flagship product: the community standard vocabulary of cell types, used across single-cell and spatial atlases.
• Uberon — the cross-species anatomy ontology, to which we are major contributors.

Taxonomies#

• Cell-type taxonomies — data-driven taxonomies of mammalian brain cell types (Whole Mouse Brain v1 & v2, primate basal ganglia) built with the BRAIN Initiative Cell Census Network (BICAN).

Knowledge graphs#

• Single Cell Knowledge Graph — a queryable graph of cell type annotations, ontology structure and associated genes.

Standards & tools#

• Cell Annotation Schema (CAS), CAS-tools and MapMyCells2CL — a standard and tools for recording, validating and reusing cell type annotations and the evidence behind them.

Agentic AI workflows#

• ask-census, Atlas-reporter and evidencell — evidence-grounded AI tools for querying atlases, interpreting cell types, and recording annotation evidence.

We also contribute to shared open infrastructure including the Ontology Development Kit, Dead Simple OWL Design Patterns, and the Ontology Lookup Service (OLS).