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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Detalhes bibliográficos
Autores: Egaña Aranguren, Mikel, Rodríguez González, Alejandro, Wilkinson, Mark D.
Tipo de documento: artigo
Data de publicação:2014
País:España
Recursos:Universidad del País Vasco
Repositório:Addi. Archivo Digital para la Docencia y la Investigación
OAI Identifier:oai:addi.ehu.eus:10810/15997
Acesso em linha:http://hdl.handle.net/10810/15997
Access Level:Acceso aberto
Palavra-chave:galaxy
web services
SADI
RDF
SPARQL
OWL
life sciences
genes
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spelling Executing SADI services in GalaxyEgaña Aranguren, MikelRodríguez González, AlejandroWilkinson, Mark D.galaxyweb servicesSADIRDFSPARQLOWLlife sciencesgenesBackground: 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.Mikel Egana Aranguren is funded by the Marie Curie Cofund programme (FP7) of the European Union and the Genomic Resources Group of the University of Basque Country. Alejandro Rodriguez Gonzalez and Mark D. Wilkinson are funded by the Isaac Peral Programme of the CBGP-UPM.Biomed Central201520152014info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10810/15997reponame:Addi. Archivo Digital para la Docencia y la Investigacióninstname:Universidad del País VascoIngléshttp://www.jbiomedsem.com/content/5/1/42/abstractinfo:eu-repo/semantics/openAccess© 2014 Egaña Aranguren et al.; licensee 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.oai:addi.ehu.eus:10810/159972026-06-18T09:23:17Z
dc.title.none.fl_str_mv Executing SADI services in Galaxy
title Executing SADI services in Galaxy
spellingShingle Executing SADI services in Galaxy
Egaña Aranguren, Mikel
galaxy
web services
SADI
RDF
SPARQL
OWL
life sciences
genes
title_short 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_sort Executing SADI services in Galaxy
dc.creator.none.fl_str_mv Egaña Aranguren, Mikel
Rodríguez González, Alejandro
Wilkinson, Mark D.
author Egaña Aranguren, Mikel
author_facet Egaña Aranguren, Mikel
Rodríguez González, Alejandro
Wilkinson, Mark D.
author_role author
author2 Rodríguez González, Alejandro
Wilkinson, Mark D.
author2_role author
author
dc.subject.none.fl_str_mv galaxy
web services
SADI
RDF
SPARQL
OWL
life sciences
genes
topic galaxy
web services
SADI
RDF
SPARQL
OWL
life sciences
genes
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.
publishDate 2014
dc.date.none.fl_str_mv 2014
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10810/15997
url http://hdl.handle.net/10810/15997
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://www.jbiomedsem.com/content/5/1/42/abstract
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Biomed Central
publisher.none.fl_str_mv Biomed Central
dc.source.none.fl_str_mv reponame:Addi. Archivo Digital para la Docencia y la Investigación
instname:Universidad del País Vasco
instname_str Universidad del País Vasco
reponame_str Addi. Archivo Digital para la Docencia y la Investigación
collection Addi. Archivo Digital para la Docencia y la Investigación
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300724

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