A tutorial on protein ontology resources for proteomic studies.

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 full-length level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or posttranslational modifications, and protein complexes. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In addition, the representation of specific protein types, such as a phosphorylated protein form, 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. PRO is manually curated starting with content derived from scientific literature. Only annotation with experimental evidence is included, and is in the form of relationship to other ontologies. In this tutorial, you will learn how to use the PRO resources to gain information about proteins of interest, such as finding conserved isoforms (ortho-isoforms), and different modified forms and their attributes. In addition, it will provide some details on how you can contribute to the ontology via the rapid annotation interface RACE-PRO.