title: The representation of protein complexes in the Protein Ontology (PRO).
abstract: BACKGROUND
  Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes.
  
  
  METHODS
  We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/.
  
  
  CONCLUSIONS
  PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species.
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME 04609, USA. carol.bult@jax.org
authors.forename: Carol J
authors.initials: CJ
authors.lastname: Bult
authors.forename: Harold J
authors.initials: HJ
authors.lastname: Drabkin
authors.forename: Alexei
authors.initials: A
authors.lastname: Evsikov
authors.forename: Darren
authors.initials: D
authors.lastname: Natale
authors.forename: Cecilia
authors.initials: C
authors.lastname: Arighi
authors.forename: Natalia
authors.initials: N
authors.lastname: Roberts
authors.forename: Alan
authors.initials: A
authors.lastname: Ruttenberg
authors.forename: Peter
authors.initials: P
authors.lastname: D'Eustachio
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.forename: Judith A
authors.initials: JA
authors.lastname: Blake
authors.forename: Cathy
authors.initials: C
authors.lastname: Wu
mesh_terms: D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D009097:Multienzyme Complexes; D046912:Multiprotein Complexes; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D009097:Multienzyme Complexes; D046912:Multiprotein Complexes; D011506:Proteins