title: OnEX: Exploring changes in life science ontologies.
abstract: BACKGROUND
  Numerous ontologies have recently been developed in life sciences to support a consistent annotation of biological objects, such as genes or proteins. These ontologies underlie continuous changes which can impact existing annotations. Therefore, it is valuable for users of ontologies to study the stability of ontologies and to see how many and what kind of ontology changes occurred.
  
  
  RESULTS
  We present OnEX (Ontology Evolution EXplorer) a system for exploring ontology changes. Currently, OnEX provides access to about 560 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.
  
  
  CONCLUSIONS
  OnEX provides a user-friendly web interface to explore information about changes in current life science ontologies. It is available at http://www.izbi.de/onex.
authors.affiliation: Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany. hartung@izbi.uni-leipzig.de
authors.forename: Michael
authors.initials: M
authors.lastname: Hartung
authors.forename: Toralf
authors.initials: T
authors.lastname: Kirsten
authors.forename: Anika
authors.initials: A
authors.lastname: Gross
authors.forename: Erhard
authors.initials: E
authors.lastname: Rahm
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D020869:Gene Expression Profiling; D020407:Internet; D012984:Software; D014584:User-Computer Interface; D018875:Vocabulary, Controlled
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D440-4
references.pmid: 17984083
references.citation: Bioinformatics. 2005 Mar;21(6):829-31
references.pmid: 15513987
references.citation: Brief Bioinform. 2004 Mar;5(1):39-55
references.pmid: 15153305
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W783-6
references.pmid: 15980585
references.citation: BMC Bioinformatics. 2006 Feb 28;7:97
references.pmid: 16507094
references.citation: Brief Bioinform. 2006 Sep;7(3):256-74
references.pmid: 16899495
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7
references.pmid: 15608251
references.citation: Stud Health Technol Inform. 2007;129(Pt 1):330-4
references.pmid: 17911733
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D599-603
references.pmid: 17135208
references.citation: J Biomed Inform. 2007 Feb;40(1):30-43
references.pmid: 16697710
references.citation: Bioinformatics. 2007 Aug 15;23(16):2198-200
references.pmid: 17545183
references.citation: Bioinformatics. 2009 Jan 15;25(2):288-9
references.pmid: 19033274
references.citation: Stud Health Technol Inform. 2006;121:279-90
references.pmid: 17095826
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D724-8
references.pmid: 18158299
references.citation: Nat Biotechnol. 2007 Nov;25(11):1251-5
references.pmid: 17989687
references.citation: AMIA Annu Symp Proc. 2007 Oct 11;:105-9
references.pmid: 18693807
references.citation: Artif Intell Med. 1999 Jan;15(1):53-76
references.pmid: 9930616
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D396-403
references.pmid: 18957448
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D690-7
references.pmid: 19033362