{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,2]],"date-time":"2024-03-02T20:58:44Z","timestamp":1709413124502},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n The exposed BioMoby functionality aids in the design of \"sensible\" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate.<\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1471-2105-7-523","type":"journal-article","created":{"date-parts":[[2006,11,30]],"date-time":"2006-11-30T19:16:49Z","timestamp":1164914209000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["BioMoby extensions to the Taverna workflow management and enactment software"],"prefix":"10.1186","volume":"7","author":[{"given":"Edward","family":"Kawas","sequence":"first","affiliation":[]},{"given":"Martin","family":"Senger","sequence":"additional","affiliation":[]},{"given":"Mark D","family":"Wilkinson","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,11,30]]},"reference":[{"issue":"4","key":"1262_CR1","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1093\/bib\/3.4.331","volume":"3","author":"MD Wilkinson","year":"2002","unstructured":"Wilkinson MD, Links M: BioMOBY: An Open Source Web Services Proposal for Biological Data. Brief Bioinform 2002, 3(4):331\u2013341. 10.1093\/bib\/3.4.331","journal-title":"Brief Bioinform"},{"key":"1262_CR2","first-page":"16","volume":"3","author":"MD Wilkinson","year":"2003","unstructured":"Wilkinson MD, Gessler DD, Farmer A, Stein L: The BioMOBY project explores open-source, simple, extensible protocols for enabling biological database interoperability. Proceedings of the Virtual Conference on Genomics and Bioinformatics 2003, 3: 16\u201326.","journal-title":"Proceedings of the Virtual Conference on Genomics and Bioinformatics"},{"key":"1262_CR3","unstructured":"The BioMoby Project Homepage[http:\/\/www.biomoby.org]"},{"key":"1262_CR4","unstructured":"The myGrid Project Homepage[http:\/\/www.mygrid.org.uk]"},{"issue":"Suppl 1","key":"1262_CR5","first-page":"i302","volume":"19","author":"R Stevens","year":"2003","unstructured":"Stevens R, Robinson A, Goble CA: myGrid: Personalised Bioinformatics on the Information Grid. proceedings of 11th International Conference on Intelligent Systems in Molecular Biology, 29th June\u20133rd July Brisbane, Australia. Bioinformatics 2003, 19(Suppl 1):i302-i304.","journal-title":"proceedings of 11th International Conference on Intelligent Systems in Molecular Biology, 29th June\u20133rd July Brisbane, Australia. Bioinformatics"},{"key":"1262_CR6","unstructured":"The Generation Challenge Programme Web Services Development Homepage[http:\/\/moby.generationcp.org\/]"},{"issue":"17","key":"1262_CR7","doi-asserted-by":"publisher","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","volume":"20","author":"T Oinn","year":"2004","unstructured":"Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics Journal 2004, 20(17):3045\u20133054. 10.1093\/bioinformatics\/bth361","journal-title":"Bioinformatics Journal"},{"key":"1262_CR8","doi-asserted-by":"crossref","unstructured":"Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T: Taverna: a tool for building and running workflows of services. Nucleic Acids Research 2006, (34 Web Server):W729-W732.","DOI":"10.1093\/nar\/gkl320"},{"key":"1262_CR9","unstructured":"The Taverna Project Website[http:\/\/taverna.sourceforge.net\/]"},{"key":"1262_CR10","unstructured":"Web Service Description Language (WSDL)[http:\/\/www.w3c.org\/TR\/wsdl]"},{"key":"1262_CR11","unstructured":"The BioMoby Object Ontology[http:\/\/www.biomoby.org\/RESOURCES\/MOBY-S\/Objects]"},{"key":"1262_CR12","unstructured":"The BioMoby Object Structure API[http:\/\/biomoby.open-bio.org\/CVS_CONTENT\/moby-live\/Docs\/MOBY-S_API\/ObjectStructure.html]"},{"key":"1262_CR13","unstructured":"Wilkinson M: Gbrowse Moby: A web based browser for BioMoby Services. Source Code for Biology and Medicine, in press."},{"issue":"1","key":"1262_CR14","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1093\/bioinformatics\/bti740","volume":"22","author":"I Navas-Delgado","year":"2006","unstructured":"Navas-Delgado I, del Mar Rojano-Munoz M, Ramirez S, Perez AJ, Andres Leon E, Aldana-Montes JF, Trelles O: Intelligent client for integrating bioinformatics services. Bioinformatics 2006, 22(1):106\u2013111. 10.1093\/bioinformatics\/bti740","journal-title":"Bioinformatics"},{"issue":"7","key":"1262_CR15","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1093\/bioinformatics\/btl001","volume":"22","author":"S Carrere","year":"2006","unstructured":"Carrere S, Gouzy G: REMORA: A pilot in the ocean of BioMoby web-services. Bioinformatics 2006, 22(7):900\u2013901. 10.1093\/bioinformatics\/btl001","journal-title":"Bioinformatics"},{"issue":"2","key":"1262_CR16","first-page":"187","volume":"5","author":"AL Turinsky","year":"2005","unstructured":"Turinsky AL, Ah-Seng AC, Gordon PMK, Stromer JN, Taschuk ML, Xu EW, Sensen CW: Bioinformatics visualization and integration with open standards: The Bluejay genomic browser. Silico Biology 2005, 5(2):187\u2013198.","journal-title":"Silico Biology"},{"key":"1262_CR17","unstructured":"The Seahawk Applet[http:\/\/bluejay.ucalgary.ca\/seahawk\/]"},{"key":"1262_CR18","unstructured":"Taverna MOBY Plugin Tutorial[http:\/\/biomoby.org\/TavernaMOBY.htm]"},{"key":"1262_CR19","unstructured":"The BioMoby Dashboard[http:\/\/biomoby.open-bio.org\/CVS_CONTENT\/moby-live\/Java\/docs\/Dashboard.html]"},{"key":"1262_CR20","first-page":"17","volume-title":"Proceedings of Second European Semantic Web Conference, ESWC 2005, Heraklion, Crete, Greece, May\u2013June 2005","author":"P Lord","year":"2005","unstructured":"Lord P, Alper P, Wroe C, Goble C: Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery. In Proceedings of Second European Semantic Web Conference, ESWC 2005, Heraklion, Crete, Greece, May\u2013June 2005. Springer-Verlag LNCS 3532; 2005:17\u201331."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-523.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:20:40Z","timestamp":1630466440000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-523"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,11,30]]},"references-count":20,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["1262"],"URL":"http:\/\/dx.doi.org\/10.1186\/1471-2105-7-523","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.1070766.523692","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,11,30]]},"assertion":[{"value":"25 September 2006","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 November 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 November 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"523"}}
