Tutorial on Protein Ontology Resources.
The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species nonspecific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning. In the first section of this chapter, we describe the PRO framework including categories of PRO terms and the relationship of PRO to other ontologies and protein resources. Next, we provide a tutorial about the PRO website ( proconsortium.org ) where users can browse and search the PRO hierarchy, view reports on individual PRO terms, and visualize relationships among PRO terms in a hierarchical table view, a multiple sequence alignment view, and a Cytoscape network view. Finally, we describe several examples illustrating the unique and rich information available in PRO.
Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA. arighi@dbi.udel.edu.
Cecilia N
CN
Arighi
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
Harold
H
Drabkin
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
Karen R
KR
Christie
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University MedicalCenter, Washington, DC, 20007, USA.
Karen E
KE
Ross
Protein Information Resource, Georgetown University Medical Center, Washington, DC, 20007, USA.
Darren A
DA
Natale
D000818:Animals; D064229:Biological Ontologies; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D058977:Molecular Sequence Annotation; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
D011506:Proteins
Orthologs; Post-translational modification; Protein complexes; Protein ontology; Proteoforms