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Journal of Biomedical Semantics

, 5:42

First Online: 22 September 2014Received: 12 December 2013Accepted: 19 September 2014

Abstract

BackgroundIn recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools.

ResultsSADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem.

ConclusionsSADI-Galaxy bridges the gap between Galaxy, an easy to use but -static- workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.

KeywordsGalaxy Web services SADI RDF SPARQL OWL AbbreviationsRDFResource description framework

OWLWeb ontology language

SADISemantic automated discovery and integration

SPARQLSPARQL protocol and RDF query language

TSVTab separated values.

Electronic supplementary materialThe online version of this article doi:10.1186-2041-1480-5-42 contains supplementary material, which is available to authorized users.

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Author: Mikel Egaña Aranguren - Alejandro Rodríguez González - Mark D Wilkinson

Source: https://link.springer.com/







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