title: Relations as patterns: bridging the gap between OBO and OWL.
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.
  
  
  RESULTS
  we developed a method to provide definition patterns for relations between classes using OWL and describe a novel implementation of the RO based on this method. We implemented our extension in software that converts ontologies in the OBO Flatfile Format to OWL, and also provide a prototype to extract relational patterns from OWL ontologies using automated reasoning. The conversion software is freely available at http://bioonto.de/obo2owl, and can be accessed via a web interface.
  
  
  CONCLUSIONS
  explicitly defining relations permits their use in reasoning software and leads to a more flexible and powerful way of representing biomedical ontologies. Using the extended langua0067e and semantics avoids several mistakes commonly made in formalizing biomedical ontologies, and can be used to automatically detect inconsistencies. The use of our method enables the use of graph-based ontologies in OWL, and makes complex OWL ontologies accessible in a graph-based form. Thereby, our method provides the means to gradually move the representation of biomedical ontologies into formal knowledge representation languages that incorporates an explicit semantics. Our method facilitates the use of OWL-based software in the back-end while ontology curators may continue to develop ontologies with an OBO-style front-end.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. rh497@cam.ac.uk
authors.forename: Robert
authors.initials: R
authors.lastname: Hoehndorf
authors.forename: Anika
authors.initials: A
authors.lastname: Oellrich
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
authors.forename: Dietrich
authors.initials: D
authors.lastname: Rebholz-Schuhmann
authors.forename: Heinrich
authors.initials: H
authors.lastname: Herre
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D012660:Semantics; D018875:Vocabulary, Controlled
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