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The representation of protein complexes in the Protein Ontology (PRO)

Carol J Bult1*, Harold J Drabkin1, Alexei Evsikov1, Darren Natale2, Cecilia Arighi3, Natalia Roberts2, Alan Ruttenberg4, Peter D'Eustachio5, Barry Smith6, Judith A Blake1 and Cathy Wu23

Author Affiliations

1 The Jackson Laboratory, 600 Main St., Bar Harbor, ME, 04609, USA

2 Protein Information Resource, Dept of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St., NW, Washington, DC, 20007, USA

3 Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE 19711, USA

4 School of Dental Medicine, State University of New York at Buffalo, 349 Squire Hall, Buffalo, NY, 14214, USA

5 Department of Biochemistry, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA

6 Department of Philosophy and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 130 Park Hall, Amherst, NY, 12460, USA

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BMC Bioinformatics 2011, 12:371  doi:10.1186/1471-2105-12-371

Published: 19 September 2011



Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes.


We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at webcite.


PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species.