TY - JOUR
T1 - Using AberOWL for fast and scalable reasoning over BioPortal ontologies
AU - Slater, Luke
AU - Gkoutos, Georgios V.
AU - Schofield, Paul N.
AU - Hoehndorf, Robert
N1 - KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: National 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).]
PY - 2016/8/8
Y1 - 2016/8/8
N2 - Background: 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.
AB - Background: 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.
UR - http://hdl.handle.net/10754/620944
UR - http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0090-0
UR - http://www.scopus.com/inward/record.url?scp=84981194197&partnerID=8YFLogxK
U2 - 10.1186/s13326-016-0090-0
DO - 10.1186/s13326-016-0090-0
M3 - Article
C2 - 27502585
SN - 2041-1480
VL - 7
JO - Journal of Biomedical Semantics
JF - Journal of Biomedical Semantics
IS - 1
ER -