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Bioinformatics Advance Access published online on May 12, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm258
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

OBO to OWL: A Protégé OWL Tab to Read/Save OBO Ontologies

Dilvan A. Moreira *,1,2 and Mark A. Musen 1

1Stanford Medical Informatics, Stanford University School of Medicine, Stanford, CA 94002. 2 USP, São Paulo, Brazil.

*To whom correspondence should be addressed. Dr. Dilvan Moreira, E-mail: dilvan{at}gmail.com


  Abstract

The OBO format from the GO consortium is a very successful format for biomedical ontologies, including the Gene Ontology. But it lacks formal computational definitions for its constructs and tools, like DL reasoners, to facilitate ontology development/maintenance. We describe the OBO Converter, a Java tool to convert files from OBO format to OWL (and vice-versa) that can also be used as a Protégé Tab plug-in. It uses the OBO to OWL mapping provided by the NCBO (a joint effort of OBO developers and OWL experts) and offers options to ease the task of saving/reading files in both formats.

Availability: bioontology.org/tools/oboinowl/obo_converter.html

Associate Editor: Prof. Dmitrij Frishman

Received on February 21, 2007; revised on May 7, 2007; accepted on May 8, 2007

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