Executing SADI services in Galaxy

Journal of Biomedical Semantics

Mark D Wilkinson²  Alejandro Rodríguez González²  Mikel Egaña Aranguren¹ 

[1] Genomic Resources, Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena auzoa z/g, 48940 Leioa - Bilbo, Spain;Biological Informatics, Centre for Plant Biotechnology and Genomics (CBGP), Technical University of Madrid (UPM), Campus of Montegancedo, 28223 Pozuelo de Alarcón, Spain

关键词: OWL;    SPARQL;    RDF;    SADI;    Web services;    Galaxy;   

Others  :  1133533
DOI  :  10.1186/2041-1480-5-42

 received in 2013-12-12, accepted in 2014-09-19,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Egaña Aranguren et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]World Wide Web Consortium: World wide web consortium. [http://www.w3.org/ webcite]. Online; accessed 28-March-2012
• [2]W3C: RDF current status. [http://www.w3.org/standards/techs/rdf webcite]. Online; accessed 28-March-2012
• [3]W3C: OWL Web Ontology Language current status. [http://www.w3.org/standards/techs/owl webcite]. Online; accessed 28-March-2012
• [4]Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek B, Martin M, McGarvey P, Gasteiger E: Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 2009, 10(1):136. BioMed Central Full Text
• [5]Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM: The EBI RDF platform: linked open data for the life sciences. Bioinformatics 2014, 30(9):1338-1339.
• [6]Kosuge T, Mashima J, Kodama Y, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y: DDBJ progress report: a new submission system for leading to a correct annotation. Nucleic Acids Res 2013, 42(Database issue):D44-9.
• [7]Belleau F, Nolin M, Tourigny N, Rigault P, Morissette J: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008, 41(5):706-716.
• [8]Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29(1):308-311.
• [9]Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA: Online Mendelian Inheritance in Man (OMIM): a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33(Database issue):D514-7.
• [10]Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
• [11]Maloney C: RESTful API to NCBI’s Entrez Utilities (E-utilities). [http://pypi.python.org/pypi/eutils webcite]. Online; accessed 26-November-2013
• [12]Wilkinson M, Vandervalk B, McCarthy L: The semantic automated discovery and integration (SADI), web service design-pattern, API and reference implementation. J Biomed Semantics 2011, 2(1):8. BioMed Central Full Text
• [13]Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P, Bhagat J, Belhajjame K, Bacall F, Hardisty A, de la Hidalga AN, Balcazar Vargas MP, Sufi S, Goble C: The Taverna workflow suite: designing and executing workflows of web services on the desktop, web or in the cloud. Nucleic Acids Res 2013, 41(W1):557-561.
• [14]IO Informatics: IO Informatics Sentient Knowledge Explorer. [http://www.io-informatics.com/products/sentient-KE.html webcite]. Online; accessed 26-November-2013
• [15]Goecks J, Nekrutenko A, Taylor J, Galaxy Team: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):86. BioMed Central Full Text
• [16]Galaxy project: Galaxy Tool XML File. [http://wiki.g2.bx.psu.edu/Admin/Tools/ToolConfigSyntax webcite]. Online; accessed 28-March-2012
• [17]Bizer C, Heath T, Berners-Lee T: Linked data - the story so far. Int J Semantic Web Inf Syst (IJSWIS) 2009, 5(3):1-22.
• [18]Aranguren ME: SADI generic. [http://toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sadi_generic/ webcite]. Online; accessed 26-November-2013
• [19]W3C: SPARQL current status. [http://www.w3.org/standards/techs/sparql webcite]. Online; accessed 28-March-2012
• [20]Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucleic Acids Res 2000, 28(1):235-242.
• [21]Sem4j: SPARQL tools. [http://toolshed.g2.bx.psu.edu/repos/sem4j/sparql_tools webcite]. Online; accessed 26-November-2013
• [22]Aranguren ME: SPARQL Galaxy. [http://toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sparql_galaxy webcite]. Online; accessed 26-November-2013
• [23]SADI: UniProt record SADI input OWL class. [http://purl.oclc.org/SADI/LSRN/UniProt_Record webcite]. Online; accessed 28-March-2012
• [24]Kasprzyk A: BioMart: driving a paradigm change in biological data management. Database 2011, 2011(0):049.
• [25]Dhamanaskar A, Cotterell ME, Zheng JZ, Miller JA, Kissinger JC, Stoeckert CJ: Suggestions in galaxy workflow design based on ontologically annotated services. In Proceedings of the 7th International Conference on Formal Ontology in Information Systems (FOIS’12). Amsterdam, The Netherlands: IOS press; 2012:29-42.
• [26]Wang R, Brewer D, Shastri S, Swayampakula S, Miller JA, Kraemer ET, Kissinger JC: Adapting the galaxy bioinformatics tool to support semantic web service composition. In Proceedings of the 2009 Congress on Services - Part I. NYC, USA: ACM; 2009:283-290.
• [27]Abouelhoda M, Issa S, Ghanem M: Tavaxy: Integrating taverna and galaxy workflows with cloud computing support. BMC Bioinformatics 2012, 13(1):77. BioMed Central Full Text