Abstract
Support for automated service discovering and workflow composition is increasingly important as the number of Web Services and data types in bioinformatics and biomedicine grows. jORCA is a desktop client able to discover and invoke Web Services published in different types of service metadata repositories. In this paper, we report that jORCA is now able to discover, compose, edit, store, export and enact workflows. As proof of concept, we present a case study which re-creates a published workflow to demonstrate new functionality in jORCA, starting from service discovery, workflow generation and refinement; to enactment, monitoring and visualization of results. The system has been exhaustively tested and documented and is freely available at http://www.bitlab-es.com/jorca.
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References
BioMoby Dashboard, http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html (accessed 2010-07-08)
Cardoso, J., Sheth, A.: Semantic e-workflow composition. Journal of Intelligent Information Systems 21(3), 191–225 (2003)
Carrere, S., Gouzy, J.: Remora: a pilot in the ocean of BioMOBY web-services. Bioinformatics 22, 900–901 (2006)
DiBernardo, M., Pottinger, R., Wilkinson, M.: Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. Journal of Biomedical Informatics 41, 837–847 (2008)
EDAM ontology, http://edamontology.sourceforge.net/ (accessed 2010-08-04)
Goble, C., et al.: BioCatalogue: A Curated Web Service Registry for the Life Science Community; Communication Data Integration in Life Sciences (DILS) 2009 - ENFIN Collocated Workshop, Manchester, UK (2009)
Gordon, P.M.K., Sensen, C.W.: Seahawk: Moving Beyond HTML in Web-based Bioinformatics Analysis. BMC Bioinformatics 8, 208 (2007)
Gordon, P., Sensen, C.: A Pilot Study into the Usability of a Scientific Workflow Construction Tool (2007), http://hdl.handle.net/1880/46486
Han, M.V., Zmasek, C.M.: phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10, 356 (2009)
Kawas, E., et al.: BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics 7, 523 (2006)
Kerhornou, A., Guigó, R.: BioMoby Web Services to support clustering of co-regulated genes based on similarity of promoter configurations. Bioinformatics 23(14), 1831–1833 (2007)
Martín-Requena, V., Ríos, J., García, M., Ramírez, S., Trelles, O.: jORCA: easily integrating bioinformatics Web Services. Bioinformatics 26(4), 553–559 (2010)
Navas-Delgado, I., et al.: Intelligent client for integrating bioinformatics services. Bioinformatics 22, 106–111 (2006)
Oinn, T., et al.: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20, 3045–3054 (2004)
Pettifer, S., et al.: An active registry for bioinformatics web services. Bioinformatics 25, 2090–2091 (2009)
Ramirez, S., et al.: A flexible framework for the design of knowledge-discovery clients. In: International Conference on Telecommunications and Multimedia (2008)
Ríos, J., Karlsson, J., Trelles, O.: Magallanes: a Web Services discovery and automatic workflow composition tool. BMC Bioinformatics 10, 334 (2009)
Romano, P., et al.: Biowep: a workflow enactment portal for bioinformatics applications. BMC Bioinformatics 8(suppl. 1), s19 (2007)
Tsiknakis, M., et al.: Building a European biomedical grid on cancer: the ACGT Integrated Project. Studies in health technology and informatics 120, 247 (2006)
Web services architecture working group, http://www.w3.org/2002/ws/arch/ (September 2006)
Wilkinson, M.D., et al.: Interoperability with Moby 1.0–it’s better than sharing your toothbrush! Briefing in Bioinformatics 9(3), 220–231 (2008)
Wilkinson, M.D.: Gbrowse moby: a web-based browser for BioMOBY services. Source Code for Biology and Medicine 1, 4 (2006)
Wolstencroft, K., et al.: The myGrid ontology: bioinformatics service discovery. Int. J. Bioinformatics Research and Applications 3(3), 303–325 (2007)
Wu, Z., et al.: Automatic composition of semantic web services using process mediation. In: Proceedings of the 9th Intl. Conf. on Enterprise Information Systems ICES (2007)
Zmasek, C.M., Eddy, S.R.: ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17, 383–384 (2001)
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Karlsson, J., Martín-Requena, V., Ríos, J., Trelles, O. (2010). Workflow Composition and Enactment Using jORCA. In: Margaria, T., Steffen, B. (eds) Leveraging Applications of Formal Methods, Verification, and Validation. ISoLA 2010. Lecture Notes in Computer Science, vol 6415. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16558-0_28
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DOI: https://doi.org/10.1007/978-3-642-16558-0_28
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