PRotein Ontology (PRO): Protein-Centric Connections of Biomedical Knowledge

The Protein Ontology (PRO) is a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins and protein complexes. The PRO website (http://www.proconsortium.org/) provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. The website functionalities include: i) browsing the ontology while displaying selected data, ii) retrieving a specific branch of the ontology, ii) searching the ontology, mappings and annotations, and iii) displaying obo stanzas for selected terms which can be used into visualization tools such as Cytoscape for an integrated view. In addition, each term has a corresponding PRO entry report that links the ontology information, the annotations and the mapping to external resources, therefore displaying all the information available for that term. For example, a term for a given complex will contain relationships and links to all the individual protein components plus annotation that applies to such complex. These functionalities, thus, allow researchers to explore interesting functional and evolutionary relationships of proteins and protein complexes as well as their higher level organization in pathways and protein networks.