OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

• Published in: Journal of biomedical semantics Vol. 4; no. 1; p. 2
• Main Authors: Aranguren, Mikel Egaña, Fernández-Breis, Jesualdo Tomás, Mungall, Chris, Antezana, Erick, González, Alejandro Rodríguez, Wilkinson, Mark D
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 04.01.2013; BioMed Central
• Subjects: Automated reasoning; Automation; BASIC BIOLOGICAL SCIENCES; Bioinformatics; biomedical ontology; Computational biology; Enrichment; existential restriction; Exploitation; Galaxies; gene ontology; Knowledge representation; Language; Life sciences; MATHEMATICS AND COMPUTING; Microprocessors; Ontology; Programming languages; Queries; Scripts; Semantic web; Semantics; Software; SPARQL query; Syntax; universal restriction
• ISSN: 2041-1480; 2041-1480
• DOI: 10.1186/2041-1480-4-2

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists' toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy's capability for enriching, modifying and querying biomedical ontologies. Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.