Applying ontology design patterns to the implementation of relations in GENIA
Abstract
Motivation: Annotated reference corpora such as the GENIA corpus play an important role in biomedical infor-mation extraction. A semantic annotation of the natural language texts in these reference corpora using formalontologies and logic is challenging due to the ambiguous use of natural language and natural language semantics.Providing formal definitions and axioms for these relations would offer the means for developing consistent andverifiable annotation guidelines and allow for the automatic verification of annotations as well as enabling thediscovery of new information through deductive inferences.Results: We developed a formal ontology of relations based on the relations used in the recent GENIA corpusannotations. For this purpose, we selected existing axiom systems based on the desired properties of the relationswithin the domain and provided new axioms for several relations. To apply this ontology of relations to thesemantic annotation of natural language texts, we developed and implemented two ontology design patterns. Weprovide an implementation of the ontology of relations in the Web Ontology Language (OWL). By combining theimplementation of the design patterns and that of the relation ontology, we also provide a software applicationto convert annotated GENIA abstracts into OWL ontologies. In this way, we make these ontologies amenable forautomated verification, deductive inferences and other knowledge-based applications.Availability: Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/.Contact: rh497@cam.ac.uk