An ontology for cell types

Abstract

We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.

Figure 1

A screenshot of the cell ontology, as seen within the OBO-Edit program, displaying all the information associated with the term hepatocyte. The left-hand panel shows all the top-level terms, together with the location of hepatocyte within the cell_by_histology classification. The right-hand panel shows all the hierarchies within which hepatocyte can be found. The top part of the central panel illustrates how the term is found, while the lower part gives the definition, the unique Cell Ontology ID and the MESH ID.