2006 FrameworkforaProteinOntology

(Natale et al., 2006) ⇒ Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H. Wu. (2006). “Framework for a Protein Ontology.” In: Proceedings of the 1st international workshop on Text mining in bioinformatics. doi:10.1145/1183535.1183544

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Author Keywords

GO; OBO; OBO foundry; PANTHER; PIRSF; Pfam; SCOP; ontology; protein

Abstract

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies -- one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway (http://pir.georgetown.edu/pro).

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	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2006 FrameworkforaProteinOntology	Hongfang Liu Barry Smith Darren A. Natale Cecilia N. Arighi Winona Barker Judith Blake Ti-Cheng Chang Zhangzhi Hu Cathy H. Wu			Framework for a Protein Ontology				10.1145/1183535.1183544