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. Terms are organised from broad classes down to specific subtypes (examples given for each):

• Neurons: excitatory, inhibitory, dopaminergic, serotonergic, cholinergic, glutamatergic, GABAergic
• Interneurons: parvalbumin+, somatostatin+, VIP+
• Astrocytes: fibrous, protoplasmic
• Oligodendrocytes: mature myelinating, oligodendrocyte precursor cells (OPCs)
• Microglia: homeostatic, activated, disease-associated
• Ependymal cells, radial glia, neural stem cells
• Vascular cells: endothelial cells, pericytes, smooth muscle cells

Connections

• Part of: OBO Foundry
• Integrates with: UBERON (anatomy), GO (molecular function), 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)