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.