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Bioinformatics. 2008 Mar 15;24(6):885-7. doi: 10.1093/bioinformatics/btn042. Epub 2008 Feb 1.

ONTO-PERL: an API for supporting the development and analysis of bio-ontologies.

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  • 1Department of Plant Systems Biology, VIB, Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium.



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.


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.


The source code code as well as sample usage scripts can be found at:

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