TGF-beta signaling proteins and the Protein Ontology

BMC Bioinformatics 10 (Suppl 5):S3 (2009)
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The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses.
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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
An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Maria, Masci Anna; Arighi Cecilia, N.; Diehl Alexander, D.; Lieberman Anne, E.; Chris, Mungall; Scheuermann Richard, H.; Smith, Barry & Cowell Lindsay, G.
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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An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci, Anna Maria; Arighi, Cecilia N.; Diehl, Alexander D.; E. Liebermann, Anne; Mungall, Chris; Scheuermann, Richard H.; Smith, Barry & Cowell, Lindsay

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