Framework for a protein ontology.
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 describe properties that can be attributed to proteins. For example, protein functions are described by the Gene Ontology (GO) and human diseases by SNOMED CT or ICD10. There is, however, a gap in the current set of ontologies - one that describes the protein entities themselves and their relationships. We have designed the 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 modifications). PRO will allow the specification of relationships between PRO, GO and other ontologies in the OBO Foundry. Here we describe the initial development of PRO, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways.
Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA. dan5@georgetown.edu
Darren A
DA
Natale
Cecilia N
CN
Arighi
Winona C
WC
Barker
Judith
J
Blake
Ti-Cheng
TC
Chang
Zhangzhi
Z
Hu
Hongfang
H
Liu
Barry
B
Smith
Cathy H
CH
Wu
D003628:Database Management Systems; D030562:Databases, Protein; D019143:Evolution, Molecular; D016247:Information Storage and Retrieval / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods; D017421:Sequence Analysis / Q000379:methods*; D014584:User-Computer Interface
D011506:Proteins