OnEX: Exploring changes in life science ontologies.
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.
Hartung
Michael
M
Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany. hartung@izbi.uni-leipzig.de
Kirsten
Toralf
T
Gross
Anika
A
Rahm
Erhard
E
D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D020869:Gene Expression Profiling; D020407:Internet; D012984:Software; D014584:User-Computer Interface; D018875:Vocabulary, Controlled
Nucleic Acids Res. 2008 Jan;36(Database issue):D440-4
17984083
Bioinformatics. 2005 Mar;21(6):829-31
15513987
Brief Bioinform. 2004 Mar;5(1):39-55
15153305
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W783-6
15980585
BMC Bioinformatics. 2006 Feb 28;7:97
16507094
Brief Bioinform. 2006 Sep;7(3):256-74
16899495
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7
15608251
Stud Health Technol Inform. 2007;129(Pt 1):330-4
17911733
Nucleic Acids Res. 2007 Jan;35(Database issue):D599-603
17135208
J Biomed Inform. 2007 Feb;40(1):30-43
16697710
Bioinformatics. 2007 Aug 15;23(16):2198-200
17545183
Bioinformatics. 2009 Jan 15;25(2):288-9
19033274
Stud Health Technol Inform. 2006;121:279-90
17095826
Nucleic Acids Res. 2008 Jan;36(Database issue):D724-8
18158299
Nat Biotechnol. 2007 Nov;25(11):1251-5
17989687
AMIA Annu Symp Proc. 2007 Oct 11;:105-9
18693807
Artif Intell Med. 1999 Jan;15(1):53-76
9930616
Nucleic Acids Res. 2009 Jan;37(Database issue):D396-403
18957448
Nucleic Acids Res. 2009 Jan;37(Database issue):D690-7
19033362