Protein Ontology (PRO) for integration of knowledge on proteins, complexes and PTMs

The Protein Ontology (PRO) is a reference ontology for proteins within the OBO Foundry, providing a structured representation of evolutionarily-related protein classes (ProEvo), multiple protein forms of a gene (ProForm) and protein complexes (ProComp). PRO connects with other ontologies and knowledge sources through mappings and definitions of relations to facilitate semantic integration of biological knowledge. The PRO ontological hierarchy in graphical network visualization allows one to seamlessly identify the relationships among different specific protein forms (such as isoforms and modified forms) and their complexes; and along with the annotation, to explore functional implications of various protein forms in pathway and network context. The PRO website provides functionalities for ontology browsing, searching, and visual display, as well as term request and community annotation. A plant-specific use case will be presented.