Open Access Highly Accessed Open Badges Software

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

Mikel Egaña Aranguren12*, Jesualdo Tomás Fernández-Breis3, Chris Mungall4, Erick Antezana5, Alejandro Rodríguez González2 and Mark D Wilkinson2

Author Affiliations

1 Ontology Engineering Group, School of Computer Science, Technical University of Madrid (UPM), Boadilla del Monte, 28660, Spain

2 Biological Informatics Group, Centre for Plant Biotechnology and Genomics (CBGP), Technical University of Madrid (UPM), Pozuelo de Alarcón, 28223, Spain

3 School of Computer Science, University of Murcia (UM), Murcia, 30100, Spain

4 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US

5 Department of Biology, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim, N-7491, Norway

For all author emails, please log on.

Journal of Biomedical Semantics 2013, 4:2  doi:10.1186/2041-1480-4-2

Published: 4 January 2013



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.