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Bioinformatics Advance Access published online on February 1, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn042
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

ONTO-PERL: An API supporting the development and analysis of bio-ontologies

E. Antezana 1,2,*, M. Egaña 3, B. De Baets 4, M. Kuiper 1,2 and V. Mironov 1,2

1Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
3University of Manchester, School of Computer Science, Oxford Road, M13 9PL Manchester, UK
4Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure links 653, 9000 Gent, Belgium

*To whom correspondence should be addressed. Mr. Erick Antezana, E-mail: erant{at}psb.ugent.be


  Abstract

Motivation: Many biomedical ontologies use OBO or OWL as knowledge representation language. The rapid increase of such ontologies calls for adequate tools to facilitate their use. In particular, there is a pressing need to programmatically deal with such ontologies in many applications, including data integration, text mining, as well as semantic applications supporting translational research.

Results: We present an Application Programming Interface (API) called ONTO-PERL. This API significantly extends the repertoire of available tools supporting the development and analysis of bioontologies.

Availability: The source code as well as sample usage scripts can be found at: http://search.cpan.org/dist/ONTO-PERL/.

Contact: erick.antezana{at}psb.ugent.be

Associate Editor: Dr.Alex Bateman

Received on October 28, 2007; revised on December 27, 2007; accepted on January 25, 2008

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