The Protein Ontology: a structured representation of protein forms and complexes

Nucleic Acids Res. 2011 Jan;39(Database issue):D539-45. doi: 10.1093/nar/gkq907. Epub 2010 Oct 8.


The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein research. PRO ( is part of the Open Biomedical Ontology Foundry.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Databases, Protein*
  • Escherichia coli Proteins / chemistry
  • Humans
  • Mice
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / classification
  • Protein Isoforms / chemistry
  • Protein Isoforms / classification
  • Proteins / chemistry
  • Proteins / classification*
  • Proteins / genetics
  • User-Computer Interface
  • Vocabulary, Controlled


  • Escherichia coli Proteins
  • Multiprotein Complexes
  • Protein Isoforms
  • Proteins