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Using AberOWL for fast and scalable reasoning over BioPortal ontologies

Published version
Peer-reviewed

Type

Article

Change log

Authors

Slater, L 
Gkoutos, GV 
Schofield, PN 
Hoehndorf, R 

Abstract

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.

Description

Keywords

AberOWL, description logics, OWL, ontology, reasoning, scalable reasoning

Journal Title

Journal of Biomedical Semantics

Conference Name

Journal ISSN

2041-1480
2041-1480

Volume Title

7

Publisher

BioMed Central