OWLDEF: Integrating OBO and OWL

An integration of the OBO Flatfile Format and the Web Ontology Language OBOF with OWL while maintaining the semantics for relations provided by the RO. (OWL) would enable automated reasoning, inferences and consistency checking of biomedical ontologies and support the development and maintenance of ontologies developed in the OBO Flatfile Format. So far, the translation of relations in the OBO language to OWL is performed according to a single rigid pattern and in violation of the relation definitions of the OBO Relationship Ontology. We extend both the OBO Flatfile Format and the Manchester OWL Syntax to accommodate relation definitions. Based on these extensions, we implemented and evaluated two software applications. The first converts the OBO Flatfile Format to an OWL representation. The second uses automated inferences to convert OWL ontologies back to a representation in the OBO Flatfile Format. The OWLDEF method is generally applicaple whenever ontologies are developed primarily using patterns and not a detailled knowledge representation language. The tools and libraries we developed for the OWLDEF method are available from http://bioonto. de/obo2owl.