title: OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.
abstract: BACKGROUND
  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.
authors.affiliation: Ontology Engineering Group, School of Computer Science, Technical University of Madrid (UPM), Boadilla del Monte, 28660, Spain. mikel.egana.aranguren@upm.es.
authors.forename: Mikel Egaña
authors.initials: ME
authors.lastname: Aranguren
authors.forename: Jesualdo Tomás
authors.initials: JT
authors.lastname: Fernández-Breis
authors.forename: Chris
authors.initials: C
authors.lastname: Mungall
authors.forename: Erick
authors.initials: E
authors.lastname: Antezana
authors.forename: Alejandro Rodríguez
authors.initials: AR
authors.lastname: González
authors.forename: Mark D
authors.initials: MD
authors.lastname: Wilkinson