A common layer of interoperability for biomedical ontologies based on OWL EL
Open Access
- 21 February 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 27 (7), 1001-1008
- https://doi.org/10.1093/bioinformatics/btr058
Abstract
Motivation: Ontologies are essential in biomedical research due to their ability to semantically integrate content from different scientific databases and resources. Their application improves capabilities for querying and mining biological knowledge. An increasing number of ontologies is being developed for this purpose, and considerable effort is invested into formally defining them in order to represent their semantics explicitly. However, current biomedical ontologies do not facilitate data integration and interoperability yet, since reasoning over these ontologies is very complex and cannot be performed efficiently or is even impossible. We propose the use of less expressive subsets of ontology representation languages to enable efficient reasoning and achieve the goal of genuine interoperability between ontologies. Results: We present and evaluate EL Vira, a framework that transforms OWL ontologies into the OWL EL subset, thereby enabling the use of tractable reasoning. We illustrate which OWL constructs and inferences are kept and lost following the conversion and demonstrate the performance gain of reasoning indicated by the significant reduction of processing time. We applied EL Vira to the open biomedical ontologies and provide a repository of ontologies resulting from this conversion. EL Vira creates a common layer of ontological interoperability that, for the first time, enables the creation of software solutions that can employ biomedical ontologies to perform inferences and answer complex queries to support scientific analyses. Availability and implementation: The EL Vira software is available from http://el-vira.googlecode.com and converted OBO ontologies and their mappings are available from http://bioonto.gen.cam.ac.uk/el-ont. Contact:rh497@cam.ac.ukKeywords
This publication has 28 references indexed in Scilit:
- Evolution of the Sequence Ontology terms and relationshipsJournal of Biomedical Informatics, 2011
- Interoperability between phenotype and anatomy ontologiesBioinformatics, 2010
- Relations as patterns: bridging the gap between OBO and OWLBMC Bioinformatics, 2010
- A set of ontologies to drive tools for the control of vector-borne diseasesJournal of Biomedical Informatics, 2010
- Cross-product extensions of the Gene OntologyJournal of Biomedical Informatics, 2010
- Applying the functional abnormality ontology pattern to anatomical functionsJournal of Biomedical Semantics, 2010
- BioPortal: ontologies and integrated data resources at the click of a mouseNucleic Acids Research, 2009
- The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary DiseaseAmerican Journal of Human Genetics, 2008
- The OBO Foundry: coordinated evolution of ontologies to support biomedical data integrationNature Biotechnology, 2007
- Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologiesBMC Bioinformatics, 2007