Cell Ontology (CL)

Overview

The Cell Ontology (CL) is the OBO Foundry standard ontology for describing cell types across all organisms. It provides a controlled vocabulary of approximately 2,500 cell type terms as of 2024, organised in parent-child relationships so that querying a broad term such as “neuron” retrieves all its subtypes.

Neuroscience Coverage

CL has detailed coverage of neural and glial cell types, organised from broad classes down to specific subtypes.

• Neuronal types covered include excitatory, inhibitory, dopaminergic, serotonergic, cholinergic, glutamatergic, and GABAergic neurons.
• Interneuron subtypes covered include parvalbumin+, somatostatin+, and VIP+ interneurons.
• Glial types covered include fibrous and protoplasmic astrocytes, myelinating oligodendrocytes, oligodendrocyte precursor cells (OPCs), homeostatic and activated microglia, and disease-associated microglia.
• Additional neural cell types covered include ependymal cells, radial glia, neural stem cells, endothelial cells, pericytes, and smooth muscle cells.

Connections

• endorsedBy: OBO Foundry
• relatedTo: UBERON (anatomy)
• relatedTo: GO (molecular function)
• relatedTo: HPO (phenotypes)

Resources

• https://cell-ontology.github.io
• https://obofoundry.org/ontology/cl.html (OBO Foundry CL page)
• https://www.ebi.ac.uk/ols/ontologies/cl (EBI Ontology Lookup Service)
• https://cellxgene.cziscience.com (CELLxGENE — requires CL annotations)