Using AberOWL for fast and scalable reasoning over BioPortal ontologies
KAUST DepartmentBio-Ontology Research Group (BORG)
Computational Bioscience Research Center
Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Online Publication Date2016-08-08
Print Publication Date2016-12
Permanent link to this recordhttp://hdl.handle.net/10754/620944
MetadataShow full item record
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.
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.
SponsorsNational 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).]
JournalJournal of Biomedical Semantics
- Aber-OWL: a framework for ontology-based data access in biology.
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- Issue date: 2015 Jan 28
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- Authors: Lamy JB
- Issue date: 2017 Jul
- Reasoning with bio-ontologies: using relational closure rules to enable practical querying.
- Authors: Blondé W, Mironov V, Venkatesan A, Antezana E, De Baets B, Kuiper M
- Issue date: 2011 Jun 1
- Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.
- Authors: Jupp S, Stevens R, Hoehndorf R
- Issue date: 2012 Apr 24
- Relations as patterns: bridging the gap between OBO and OWL.
- Authors: Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H
- Issue date: 2010 Aug 31