title: Using AberOWL for fast and scalable reasoning over BioPortal ontologies.
abstract: Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most other tools utilizing ontologies, either provide access to ontologies without use of automated reasoning, or limit the number of ontologies for which automated reasoning-based access is provided.
  
  
  
  We apply the AberOWL infrastructure to provide automated reasoning-based access to all accessible and consistent ontologies in BioPortal (368 ontologies). We perform an extensive performance evaluation to determine query times, both for queries of different complexity and for queries that are performed in parallel over the ontologies.
  
  
  
  We demonstrate that, with the exception of a few ontologies, even complex and parallel queries can now be answered in milliseconds, therefore allowing automated reasoning to be used on a large scale, to run in parallel, and with rapid response times.
authors: College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom. lxs511@bham.ac.uk.
authors: Luke
authors: L
authors: Slater
authors: College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom.|Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TT, United Kingdom.
authors: Georgios V
authors: GV
authors: Gkoutos
authors: Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, England, CB2 3EG, United Kingdom.
authors: Paul N
authors: PN
authors: Schofield
authors: Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia.
authors: Robert
authors: R
authors: Hoehndorf
mesh_terms: D064229:Biological Ontologies; D012660:Semantics; D013997:Time Factors
keywords: AberOWL; Description logics; OWL; Ontology; Reasoning; Scalable reasoning