jORCA and Magallanes Sailing Together towards Integration of Web Services

  • Johan Karlsson
  • Oswaldo Trelles
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6620)


It becomes increasingly important to support automated service discovering and composition due to the growing number of Web Services and data types in bioinformatics and biomedicine. jORCA is a user-friendly desktop client which is able to discover and invoke Web Services from different metadata repositories for services. This paper demonstrates the usefulness of jORCA for service composition by recreating a previously published workflow, starting with the discovery of data types, service composition (workflow generation) and refinement; to enactment, monitoring and visualization of results. The system has been exhaustively tested and documented and is freely available at .


Service Composition Service Discovery Metadata Repository Output Data Type Promoter Configuration 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    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)CrossRefGoogle Scholar
  2. 2.
    Gordon, P.M.K., Sensen, C.W.: Seahawk: Moving Beyond HTML in Web-based Bioinformatics Analysis. BMC Bioinformatics 8, 208 (2007)CrossRefGoogle Scholar
  3. 3.
    Karlsson, J., Martín-Requena, V., Ríos, J., Trelles, O.: Workflow Composition and Enactment Using jORCA. In: Margaria, T., Steffen, B. (eds.) ISoLA 2010. LNCS, vol. 6415, pp. 328–339. Springer, Heidelberg (2010), doi:10.1007/978-3-642-16558-0_28CrossRefGoogle Scholar
  4. 4.
    Kawas, E., et al.: BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics 7, 523 (2006)CrossRefGoogle Scholar
  5. 5.
    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)CrossRefGoogle Scholar
  6. 6.
    Martín-Requena, V., Ríos, J., García, M., Ramírez, S., Trelles, O.: Jorca: easily integrating bioinformatics Web Services. Bioinformatics 26(4), 553–559 (2010)CrossRefGoogle Scholar
  7. 7.
    MOBY Central at the University of Calgary,
  8. 8.
    MOBY Central at University of Malaga,
  9. 9.
    Navas-Delgado, I., et al.: Intelligent client for integrating bioinformatics services. Bioinformatics 22, 106–111 (2006)CrossRefGoogle Scholar
  10. 10.
    Ramirez, S., et al.: A flexible framework for the design of knowledge-discovery clients. In: International Conference on Telecommunications and Multimedia (2008)Google Scholar
  11. 11.
    Ríos, J., Karlsson, J., Trelles, O.: Magallanes: a Web Services discovery and automatic workflow composition tool. BMC Bioinformatics 10, 334 (2009)CrossRefGoogle Scholar
  12. 12.
    Tsiknakis, M., et al.: Building a European biomedical grid on cancer: the ACGT Integrated Project. Studies in Health Technology and Informatics 120, 247 (2006)Google Scholar
  13. 13.
    Web services architecture working group (September 2006),
  14. 14.
    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)CrossRefGoogle Scholar
  15. 15.
    Wilkinson, M.D.: Gbrowse moby: a web-based browser for BioMOBY services. Source Code for Biology and Medicine 1, 4 (2006)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Johan Karlsson
    • 1
  • Oswaldo Trelles
    • 2
  1. 1.Fundación IMABISMálagaSpain
  2. 2.Computer Architecture DepartmentUniversity of MálagaMálagaSpain

Personalised recommendations