The representation of protein complexes in the Protein Ontology

BMC Bioinformatics 12 (371):1-11 (2011)
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Abstract
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 http://pir.georgetown.edu/pro/.
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References found in this work BETA
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration.Smith, Barry; Ashburner, Michael; Rosse, Cornelius; Bard, Jonathan; Bug, William; Ceusters, Werner; Goldberg, Louis J.; Eilbeck, Karen; Ireland, Amelia; Mungall, Christopher J.; Leontis, Neocles & Others,
Relations in Biomedical Ontologies.Smith, Barry; Ceusters, Werner; Klagges, Bert; Köhler, Jacob; Kuma, Anand; Lomax, Jane; Mungall, ; Neuhaus, Fabian; Rector, Alan & Rosse, Cornelius
The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Natale, Darren; Arighi, Cecilia N.; Barker, Winona C.; Blake, Judith A.; Bult, Carol J.; Caudy, Michael; Drabkin, Harold J.; D’Eustachio, Peter; Evsikov, Alexei V.; Huang, Hongzhan; Nchoutmboube, Jules; Roberts, Natalia V.; Smith, Barry; Zhang, Jian & Wu, Cathy H.
National Center for Biomedical Ontology: Advancing Biomedicine Through Structured Organization of Scientific Knowledge.Rubin, Daniel L.; Lewis, Suzanna E.; Mungall, Chris J.; Sima, Misra; Monte, Westerfield; Michael, Ashburner; Chute, Christopher G.; Sim, Ida; Solbrig, Harold; Storey, M. A.; Smith, Barry; Richter, John D.; Noy, Natasha & Musen, Mark A.
Framework for a Protein Ontology.Natale, Darren A.; Arighi, Cecilia N.; Barker, Winona; Blake, Judith; Chang, Ti-Cheng; Hu, Zhangzhi; Liu, Hongfang; Smith, Barry & Wu, Cathy H.

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Citations of this work BETA
Ontologies as Integrative Tools for Plant Science.Walls, Ramona; Athreya, Balaji; Cooper, Laurel; Elser, Justin; Gandolfo, Maria A.; Jaiswal, Pankaj; Mungall, Christopher J.; Preece, Justin; Rensing, Stefan; Smith, Barry & Stevenson, Dennis W.
Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.Arighi, Cecilia; Shamovsky, Veronica; Masci, Anna Maria; Ruttenberg, Alan; Smith, Barry; Natale, Darren; Wu, Cathy & D’Eustachio, Peter
Protein Ontology: A Controlled Structured Network of Protein Entities.Natale Darren, A.; Arighi Cecilia, N.; Blake Judith, A.; Bult Carol, J.; Christie Karen, R.; Julie, Cowart; Peter, D’Eustachio; Diehl Alexander, D.; Drabkin Harold, J.; Olivia, Helfer; Smith, Barry & Others,

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