The Protein Ontology: a structured representation of protein forms and complexes

Abstract

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontology Foundry.

Figure 1.

Overview of PRO. The left panel shows the ProEvo and ProForm subontologies, the right panel shows the ProComp subontology and the central panel shows the typical resources used to define or annotate PRO terms.

Figure 2.

PRO browser displaying the hierarchy for CD28-containing terms (partial view). (1) The Find box provides a means to display or highlight terms that match a specific word or phrase. (2) The hierarchy is displayed with term highlighted. (3) Information tabs: click on a black tab to display the information in the table (grayed-out tabs either do not apply or have already been selected for display). (4) Customizable table of selected information. In the example shown Gene, Reactome cross-reference and PMID were selected. Category is shown by default.

Figure 3.

Sample PRO entry report for a cleaved form of platelet-derived growth factor C (partial view). (1) Ontology section, with ID, name and synonyms, definition, comments and hierarchy links. (2) Sequence and features for representative entities. For cleaved forms, the underlining indicates the entity of interest while red letters (not shown in this example) indicate modified residues. (3) Mapped cross-references to the identical entity in an external resource. (4) The annotation section.