Relations as patterns: bridging the gap between OBO and OWL |
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| Authors: | Robert Hoehndorf Anika Oellrich Michel Dumontier Janet Kelso Dietrich Rebholz-Schuhmann Heinrich Herre |
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| Affiliation: | (1) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;(2) Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany;(3) Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany;(4) Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1 S 5B6, Canada;(5) Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK |
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| Abstract: | Background Most biomedical ontologies are represented in the OBO Flatfile Format, which is an easy-to-use graph-based ontology language. The semantics of the OBO Flatfile Format 1.2 enforces a strict predetermined interpretation of relationship statements between classes. It does not allow flexible specifications that provide better approximations of the intuitive understanding of the considered relations. If relations cannot be accurately expressed then ontologies built upon them may contain false assertions and hence lead to false inferences. Ontologies in the OBO Foundry must formalize the semantics of relations according to the OBO Relationship Ontology (RO). Therefore, being able to accurately express the intended meaning of relations is of crucial importance. Since the Web Ontology Language (OWL) is an expressive language with a formal semantics, it is suitable to de ne the meaning of relations accurately. |
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