OBO to OWL: a protege OWL tab to read/save OBO ontologies

Bioinformatics. 2007 Jul 15;23(14):1868-70. doi: 10.1093/bioinformatics/btm258. Epub 2007 May 12.


The Open Biomedical Ontologies (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 Web Ontology Language (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 National Center for Biomedical Ontologies (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.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Computer Graphics
  • Computers
  • Database Management Systems
  • Databases, Genetic
  • Humans
  • Information Science
  • Information Storage and Retrieval
  • Programming Languages
  • Software
  • User-Computer Interface