title: Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
abstract: BACKGROUND
  The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI.
  
  
  RESULTS
  We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI.
  
  
  CONCLUSIONS
  The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl.
authors.affiliation: Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA. david.hill@jax.org
authors.forename: David P
authors.initials: DP
authors.lastname: Hill
authors.forename: Nico
authors.initials: N
authors.lastname: Adams
authors.forename: Mike
authors.initials: M
authors.lastname: Bada
authors.forename: Colin
authors.initials: C
authors.lastname: Batchelor
authors.forename: Tanya Z
authors.initials: TZ
authors.lastname: Berardini
authors.forename: Heiko
authors.initials: H
authors.lastname: Dietze
authors.forename: Harold J
authors.initials: HJ
authors.lastname: Drabkin
authors.forename: Marcus
authors.initials: M
authors.lastname: Ennis
authors.forename: Rebecca E
authors.initials: RE
authors.lastname: Foulger
authors.forename: Midori A
authors.initials: MA
authors.lastname: Harris
authors.forename: Janna
authors.initials: J
authors.lastname: Hastings
authors.forename: Namrata S
authors.initials: NS
authors.lastname: Kale
authors.forename: Paula
authors.initials: P
authors.lastname: de Matos
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.forename: Gareth
authors.initials: G
authors.lastname: Owen
authors.forename: Paola
authors.initials: P
authors.lastname: Roncaglia
authors.forename: Christoph
authors.initials: C
authors.lastname: Steinbeck
authors.forename: Steve
authors.initials: S
authors.lastname: Turner
authors.forename: Jane
authors.initials: J
authors.lastname: Lomax
mesh_terms: D001695:Biology; D002621:Chemistry; D005796:Genes; D018875:Vocabulary, Controlled
references.citation: J Biomed Inform. 2011 Feb;44(1):80-6
references.pmid: 20152934
references.citation: Nat Biotechnol. 2007 Nov;25(11):1251-5
references.pmid: 17989687
references.citation: Genomics. 2001 May 15;74(1):121-8
references.pmid: 11374909
references.citation: Nat Chem Biol. 2007 Aug;3(8):447-50
references.pmid: 17637771
references.citation: Methods Inf Med. 2010;49(2):135-40
references.pmid: 20135080
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D525-31
references.pmid: 19850723
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D434-7
references.pmid: 14681451
references.citation: Bioinformatics. 2007 Aug 15;23(16):2198-200
references.pmid: 17545183
references.citation: Methods Mol Biol. 2007;406:495-520
references.pmid: 18287709
references.citation: Science. 2010 Jul 2;329(5987):72-5
references.pmid: 20466884
references.citation: Pac Symp Biocomput. 2003;:624-35
references.pmid: 12603063
references.citation: BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S2
references.pmid: 18460184
references.citation: Cytogenet Genome Res. 2007;117(1-4):278-87
references.pmid: 17675869
references.citation: BMC Bioinformatics. 2009 Apr 27;10:125
references.pmid: 19397794
references.citation: Nat Chem Biol. 2008 Nov;4(11):682-90
references.pmid: 18936753
references.citation: Plant Physiol. 2004 Jun;135(2):745-55
references.pmid: 15173566
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D754-60
references.pmid: 22135291
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6
references.pmid: 14681408
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D668-72
references.pmid: 16381955
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D249-54
references.pmid: 19854951
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references.pmid: 18948289
references.citation: Mol Cell Proteomics. 2010 Apr;9(4):648-55
references.pmid: 19959820
references.citation: Brief Bioinform. 2005 Sep;6(3):298-304
references.pmid: 16212777
references.citation: Curr Genomics. 2010 Apr;11(2):136-45
references.pmid: 20885821
references.citation: J Biomed Inform. 2011 Dec;44 Suppl 1:S5-S11
references.pmid: 21397722
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D735-41
references.pmid: 22067452
references.citation: Pac Symp Biocomput. 2006;:28-39
references.pmid: 17094225
references.citation: Comp Funct Genomics. 2004;5(6-7):509-20
references.pmid: 18629143
references.citation: Bioinformatics. 2008 Jun 15;24(12):1448-55
references.pmid: 18463117
references.citation: BMC Bioinformatics. 2009 Jul 21;10:228
references.pmid: 19622167