xGENIA: A comprehensive OWL ontology based on the GENIA corpus

The GENIA ontology is a taxonomy that was developed as a result of manual annotation of a subset of MEDLINE, the GENIA corpus. Both the ontology and corpus have been used as a benchmark to test and develop biological information extraction tools. Recent work shows, however, that there is a demand for a more comprehensive ontology that would go along with the corpus. We propose a complete OWL ontology built on top of the GENIA ontology utilizing the GENIA corpus. The proposed ontology includes elements such as the original taxonomy of categories, biological entities as individuals, relations between individuals using verbs and verb nominalizations as object properties, and links to the UMLS Metathesaurus concepts. AVAILABILITY: http://www.ece.ualberta.ca/~rrak/ontology/xGENIA/