This article is part of the supplement: Proceedings of the Fourth International Symposium on Semantic Mining in Biomedicine (SMBM)
Research
Ontology design patterns to disambiguate relations between genes and gene products in GENIA
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* Corresponding author: Robert Hoehndorf rh497@cam.ac.uk
1 European Bioinformatics Institute, Hinxton, Cambridge, UK
2 Department of Computer Science, University of Leipzig, Leipzig, Germany
3 Department of Computer Science, University of Tokyo, Tokyo, Japan
4 Department of Genetics, University of Cambridge, UK
Journal of Biomedical Semantics 2011, 2(Suppl 5):S1 doi:10.1186/2041-1480-2-S5-S1
Published: 6 October 2011Abstract
Motivation
Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences.
Results
We provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated 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/ webcite.