Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation. 1 The Protein Ontology Resources The Protein Ontology (PRO) is a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins and protein complexes [1]. It is one of the first six ontologies recommended by the OBO Foundry as preferred targets for community convergence, alongside the Gene Ontology (GO). The PRO website (http://pir.georgetown. edu/pro/pro.shtml) 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, iii) searching the ontology, mappings and annotations, iv) displaying OBO stanzas for selected terms which can be used into visualization tools such as Cytoscape for an integrated view, and v) downloading selected terms in OWL format for import into an ontology or OWL-aware environment. 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 this complex (Fig. 1). PRO identifiers are URIs following the OBO Foundry ID Policy (http://obofoundry.org/id-policy.shtml). An example is: http://purl.obolibrary.org/obo/PR_000000000. URLs are resolvable, providing information in the web browser and linked data access [2] using Ontobee (http://ontobee.org ). PRO allows researchers to explore functional and evolutionary relationships pf proteins and protein complexes as well as their higher level organization in pathways and protein networks (Figs. 1 and 2). For example, Fig. 2 shows in a single Cytoscape view that glutaminase 1 has a paralog glutaminase 2 (both share the glutaminase domain as shown in annotation of the parent term), that both are found E.coli and B. subtilis. It also shows the acetylation of glutaminase 1 and that the active glutaminase 1 is a complex (see corresponding annotation) and it is also observed in both species. A controlled vocabulary is used for annotation and PRO interoperates with GO for PRO complexes. 285 ICBO: International Conference on Biomedical Ontology July 28-30, 2011 · Buffalo, NY, USA