title: A common layer of interoperability for biomedical ontologies based on OWL EL.
abstract: BACKGROUND
  Ontologies are essential in biomedical research due to their ability to semantically integrate content from different scientific databases and resources. Their application improves capabilities for querying and mining biological knowledge. An increasing number of ontologies is being developed for this purpose, and considerable effort is invested into formally defining them in order to represent their semantics explicitly. However, current biomedical ontologies do not facilitate data integration and interoperability yet, since reasoning over these ontologies is very complex and cannot be performed efficiently or is even impossible. We propose the use of less expressive subsets of ontology representation languages to enable efficient reasoning and achieve the goal of genuine interoperability between ontologies.
  
  
  RESULTS
  We present and evaluate EL Vira, a framework that transforms OWL ontologies into the OWL EL subset, thereby enabling the use of tractable reasoning. We illustrate which OWL constructs and inferences are kept and lost following the conversion and demonstrate the performance gain of reasoning indicated by the significant reduction of processing time. We applied EL Vira to the open biomedical ontologies and provide a repository of ontologies resulting from this conversion. EL Vira creates a common layer of ontological interoperability that, for the first time, enables the creation of software solutions that can employ biomedical ontologies to perform inferences and answer complex queries to support scientific analyses.
  
  
  METHODS
  The EL Vira software is available from http://el-vira.googlecode.com and converted OBO ontologies and their mappings are available from http://bioonto.gen.cam.ac.uk/el-ont.
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, UK. rh497@cam.ac.uk
authors.forename: Robert
authors.initials: R
authors.lastname: Hoehndorf
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.forename: Anika
authors.initials: A
authors.lastname: Oellrich
authors.forename: Sarala
authors.initials: S
authors.lastname: Wimalaratne
authors.forename: Dietrich
authors.initials: D
authors.lastname: Rebholz-Schuhmann
authors.forename: Paul
authors.initials: P
authors.lastname: Schofield
authors.forename: Georgios V
authors.initials: GV
authors.lastname: Gkoutos
mesh_terms: D035843:Biomedical Research; D016208:Databases, Factual; D012660:Semantics; D012984:Software; D018875:Vocabulary, Controlled