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Bioinformatics Advance Access originally published online on February 1, 2008
Bioinformatics 2008 24(6):885-887; 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 for supporting the development and analysis of bio-ontologies

Erick Antezana 1,2,*, Mikel Egaña 3, Bernard De Baets 4, Martin Kuiper 1,2 and Vladimir Mironov 1,2

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

*To whom correspondence should be addressed.


  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 bio-ontologies.

Availability: The source code 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: Alex Bateman

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

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