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Executing SADI services in Galaxy

BACKGROUND: In 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 prov...

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Autores principales: Aranguren, Mikel Egaña, González, Alejandro Rodríguez, Wilkinson, Mark D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193140/
https://www.ncbi.nlm.nih.gov/pubmed/25309716
http://dx.doi.org/10.1186/2041-1480-5-42
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author Aranguren, Mikel Egaña
González, Alejandro Rodríguez
Wilkinson, Mark D
author_facet Aranguren, Mikel Egaña
González, Alejandro Rodríguez
Wilkinson, Mark D
author_sort Aranguren, Mikel Egaña
collection PubMed
description BACKGROUND: In 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. RESULTS: SADI-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. CONCLUSIONS: SADI-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.
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spelling pubmed-41931402014-10-11 Executing SADI services in Galaxy Aranguren, Mikel Egaña González, Alejandro Rodríguez Wilkinson, Mark D J Biomed Semantics Software BACKGROUND: In 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. RESULTS: SADI-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. CONCLUSIONS: SADI-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. BioMed Central 2014-09-22 /pmc/articles/PMC4193140/ /pubmed/25309716 http://dx.doi.org/10.1186/2041-1480-5-42 Text en © Egaña Aranguren et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Aranguren, Mikel Egaña
González, Alejandro Rodríguez
Wilkinson, Mark D
Executing SADI services in Galaxy
title Executing SADI services in Galaxy
title_full Executing SADI services in Galaxy
title_fullStr Executing SADI services in Galaxy
title_full_unstemmed Executing SADI services in Galaxy
title_short Executing SADI services in Galaxy
title_sort executing sadi services in galaxy
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193140/
https://www.ncbi.nlm.nih.gov/pubmed/25309716
http://dx.doi.org/10.1186/2041-1480-5-42
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