The Cell Component Ontology

SRI Bioinformatics Research Group     |   Carnegie Institution of Washington
Cell Component Ontology

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Overview     The Cell Component Ontology (CCO) is a controlled vocabulary of terms describing cellular components and compartments, and relationships between these terms. CCO spans all domains of life, and includes terms such as cytoplasm, cell wall, and chloroplast. The ontology currently contains 160 terms.[more]

CCO was developed to provide a controlled vocabulary of terms for annotating the subcellular locations of enzymes and compartments involved in transport reactions in the MetaCyc database, and in all Pathway/Genome Databases created using SRI's Pathway Tools software, such as the BioCyc collection of Pathway/Genome Databases.

CCO allows robust querying of enzymes, and in turn their catalyzed reactions and pathways, based on the subcellular locations of the enzymes. Example queries supported include: find pathways spanning different cell compartments; find all membrane-associated reactions; find how many subcellular membranes a compound has to cross to be converted to a final product. In addition, CCO makes it possible to graphically display enzymes, reactions, and pathways in their respective subcellular locations.

The MetaCyc database emphasizes small molecule metabolism. Therefore, only the commonly used cell component terms that are relevant to small-molecule metabolism are included.

We have adopted many terms and their definitions from the Gene Ontology (GO) and are grateful to the GO consortium for making their ontology publicly available.

We kindly thank the reviewers of CCO, Wolf Frommer, Tanya Berardini, Leonore Reiser, Ron Caspi, for their suggestions and comments.

This work was supported by grant GM70065 from the NIH National Institute for General Medical Sciences.

More Details
For more details on CCO, please see the Browse and Download areas to the left, and read this additional document.

Authors     Peifen Zhang, Suzanne Paley, Pallavi Kaipa, Seung Yon Rhee, and Peter D. Karp
How to Cite     Please cite CCO as Zhang et al., 2005, "MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research" Plant Physiology, 138: 27-37 in publications resulting from its use.

BioCyc | EcoCyc | MetaCyc | HumanCyc