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dc.contributor.authorSlater, Luke
dc.contributor.authorGkoutos, Georgios V.
dc.contributor.authorSchofield, Paul N.
dc.contributor.authorHoehndorf, Robert
dc.date.accessioned2016-10-12T09:15:25Z
dc.date.available2016-10-12T09:15:25Z
dc.date.issued2016-08-08
dc.identifier.citationSlater L, Gkoutos GV, Schofield PN, Hoehndorf R (2016) Using AberOWL for fast and scalable reasoning over BioPortal ontologies. J Biomed Semant 7. Available: http://dx.doi.org/10.1186/s13326-016-0090-0.
dc.identifier.issn2041-1480
dc.identifier.pmid27502585
dc.identifier.doi10.1186/s13326-016-0090-0
dc.identifier.urihttp://hdl.handle.net/10754/620944
dc.description.abstractBackground: 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. Methods: 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. Results and conclusions: 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.
dc.description.sponsorshipNational Science Foundation[7 LS and GVG wish to acknowledge support from the National Science Foundation (grant number: NSF IOS-1340112)., LS and GVG wish to acknowledge support from the National Science Foundation (grant number: NSF IOS-1340112).]
dc.publisherSpringer Nature
dc.relation.urlhttp://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0090-0
dc.rights© The Author(s) 2016. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.subjectAberOWL
dc.titleUsing AberOWL for fast and scalable reasoning over BioPortal ontologies
dc.typeArticle
dc.contributor.departmentBio-Ontology Research Group (BORG)
dc.contributor.departmentComputational Bioscience Research Center
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalJournal of Biomedical Semantics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionCollege of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham
dc.contributor.institutionCollege of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham
dc.contributor.institutionInstitute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust
dc.contributor.institutionDepartment of Physiology, Development and Neuroscience, University of Cambridge
kaust.personHoehndorf, Robert
refterms.dateFOA2018-06-14T05:56:43Z
dc.date.published-online2016-08-08
dc.date.published-print2016-12


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