TermGenie - a web-application for pattern-based ontology class generation.
BACKGROUND
Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes.


RESULTS
TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.


CONCLUSIONS
TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.
Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA.
Heiko
H
Dietze
The Arabidopsis Information Resource, Phoenix Bioinformatics, Redwood City, CA 94063 USA.
Tanya Z
TZ
Berardini
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD UK.
Rebecca E
RE
Foulger
Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA.
David P
DP
Hill
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD UK.
Jane
J
Lomax
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD UK.
David
D
Osumi-Sutherland
The Arabidopsis Information Resource, Phoenix Bioinformatics, Redwood City, CA 94063 USA.
Paola
P
Roncaglia
Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA.
Christopher J
CJ
Mungall
Class generation; Ontology