OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Aranguren, M. E., Fernández-Breis, J. T., Mungall, C., Antezana, E., Rodríguez González, A., & Wilkinson, M. Journal of Biomedical Semantics, Enero, 2013. oeg
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows [link]Paper  abstract   bibtex   
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.
@article{upm15232,
           month = {Enero},
           title = {OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows},
          author = {Mikel Ega{\~n}a Aranguren and Jesualdo Tom{\'a}s Fern{\'a}ndez-Breis and C. Mungall and E. Antezana and A. Rodr{\'i}guez Gonz{\'a}lez and M. Wilkinson},
            year = {2013},
            note = {oeg},
         journal = {Journal of Biomedical Semantics},
             url = {http://oa.upm.es/15232/},
        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.}
}

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