Protein Ontology and Community Curation

Abstract

The Protein Ontology (PRO) is designed as a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from the classification of proteins, on the basis of evolutionary relationships at the homeomorphic level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or post-translational modifications. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In this way PRO can be integrated with or cross-referenced by other ontologies and/or databases. The representation of specific protein entities in PRO allows precise definition of objects in pathways, complexes, or in disease modeling. This is useful for proteomics studies where isoforms and modified forms must be differentiated and for biological pathway/network representation where the cascade of events often depends on a specific protein modification. The PRO framework is designed to allow the community to curate any protein entities of interest and will provide a stable unique identifier to any protein type. PRO is manually curated starting with content derived from various data sources coupling with scientific literature. Only annotation with experimental evidence is included, and is in the form of relationship to other ontologies (such as Gene Ontology, Sequence Ontology, and PSI-MOD). We have developed a web-based curation editor for PRO community annotation. In the tutorial, we will first give a brief introduction to the ontology and its relevance to the research communities - OBO ontologies, MOD, pathway and other databases, and any resources that need references/links to protein types. We will show the components of the PRO entry report, and how to search the ontology. Then, we will walk through an example where we will teach the basic curation steps: accessing the web editor, entering the protein to be defined with source attribution, and adding functional annotation. We will provide the necessary tools and documentation so that the user will be able to start curating the protein types of interest. PRO URL: "http://pir.georgetown.edu/pro/":http://pir.georgetown.edu/pro/