Getting the Best from Two Worlds: Converting Between OBO and OWL Formats

OWL is one of the most popular ontology languages, mostly due to its expressiveness as well as its formal semantics. Yet, in the biomedical domain, OBO, a language that was expressly developed for the construction of bioontologies, is the format preferred by the community for this purpose. This is best exemplified by the fact that OBO-based ontologies are driving the model organism databases that use the common schema named Chado, a standard in the GMOD project. Thus, converting ontologies written in OWL to OBO and vice versa are crucial processes, in order to take full advantage of all resources that are being developed. In this report we describe first the hurdles that we faced while using the existing tools for converting ontologies between the two different formats. Furthermore, we present two scripts that we developed in order to overcome the recorded difficulties. A number of tests performed on several bioontologies show that these scripts are in position to successfully carry out these