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

Egaña Aranguren, Mikel and Fernández-Breis, Jesualdo Tomás and Mungall, C. and Antezana, E. and Rodríguez González, A. and Wilkinson, M. (2013). OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. "Journal of Biomedical Semantics" ;

Description

Title: OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows
Author/s:
  • Egaña Aranguren, Mikel
  • Fernández-Breis, Jesualdo Tomás
  • Mungall, C.
  • Antezana, E.
  • Rodríguez González, A.
  • Wilkinson, M.
Item Type: Article
Título de Revista/Publicación: Journal of Biomedical Semantics
Date: 4 January 2013
Subjects:
Faculty: Facultad de Informática (UPM)
Department: Inteligencia Artificial
UPM's Research Group: oeg
Creative Commons Licenses: None

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Abstract

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. Results 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. Conclusions 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.

More information

Item ID: 15232
DC Identifier: http://oa.upm.es/15232/
OAI Identifier: oai:oa.upm.es:15232
Official URL: http://www.jbiomedsem.com/content/4/1/2
Deposited by: Dr Oscar Corcho
Deposited on: 10 May 2013 05:50
Last Modified: 21 Apr 2016 15:16
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