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

Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, Wilkinson MD - J Biomed Semantics (2013)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ontology Engineering Group, School of Computer Science, Technical University of Madrid (UPM), Boadilla del Monte, 28660, Spain. mikel.egana.aranguren@upm.es.

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.

No MeSH data available.


Complex querying of GO (as shown in Galaxy). OPPL-query workflow for quering GO against GAFs. The result is a list of proteins of interest.
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Figure 8: Complex querying of GO (as shown in Galaxy). OPPL-query workflow for quering GO against GAFs. The result is a list of proteins of interest.

Mentions: OPPL-Galaxy can be combined with other Galaxy-enabled tools to build advanced workflows such as the one shown in Figures 8 and 9. This workflow can be used by a scientist to pose a complex question against GO, namely ‘What are the proteins that act on processes that involve hepatocytes and are part of or regulate other biological processes?’. Posing such a complex question requires different steps that can be performed with OPPL and stored for further analysis with the help of Galaxy.


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

Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, Wilkinson MD - J Biomed Semantics (2013)

Complex querying of GO (as shown in Galaxy). OPPL-query workflow for quering GO against GAFs. The result is a list of proteins of interest.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643862&req=5

Figure 8: Complex querying of GO (as shown in Galaxy). OPPL-query workflow for quering GO against GAFs. The result is a list of proteins of interest.
Mentions: OPPL-Galaxy can be combined with other Galaxy-enabled tools to build advanced workflows such as the one shown in Figures 8 and 9. This workflow can be used by a scientist to pose a complex question against GO, namely ‘What are the proteins that act on processes that involve hepatocytes and are part of or regulate other biological processes?’. Posing such a complex question requires different steps that can be performed with OPPL and stored for further analysis with the help of Galaxy.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ontology Engineering Group, School of Computer Science, Technical University of Madrid (UPM), Boadilla del Monte, 28660, Spain. mikel.egana.aranguren@upm.es.

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.

No MeSH data available.