Relations in biomedical ontologies

Barry Smith¹^,2 , Werner Ceusters³ , Bert Klagges⁴ , Jacob Köhler⁵ , Anand Kumar¹ , Jane Lomax⁶ , Chris Mungall⁷ , Fabian Neuhaus¹ , Alan L Rector⁸ and Cornelius Rosse⁹

¹Institute for Formal Ontology and Medical Information Science, Saarland University, D-66041 Saarbrücken, Germany

²Department of Philosophy, University at Buffalo, Buffalo, NY 14260, USA

³European Centre for Ontological Research, Saarland University, D-66041 Saarbrücken, Germany

⁴Department of Genetics, University of Leipzig, D-04103 Leipzig, Germany

⁵Rothamsted Research, Harpenden, AL5 2JQ, UK

⁶European Bioinformatics Institute, Hinxton, CB10 1SD, UK

⁷HHMI, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94729, USA

⁸Department of Computer Science, University of Manchester, M13 9PL, UK

⁹Department of Biological Structure, University of Washington, Seattle, WA 98195, USA

author email corresponding author email

Genome Biology 2005, 6:R46doi:10.1186/gb-2005-6-5-r46


Published:	28 April 2005

Subject areas: Bioinformatics, Genome studies

Abstract

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.