Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt

  • Phillip Lord
  • Sean Bechhofer
  • Mark D. Wilkinson
  • Gary Schiltz
  • Damian Gessler
  • Duncan Hull
  • Carole Goble
  • Lincoln Stein
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3298)


We have seen an increasing amount of interest in the application of Semantic Web technologies to Web services. The aim is to support automated discovery and composition of the services allowing seamless and transparent interoperability. In this paper we discuss three projects that are applying such technologies to bioinformatics: \({}^{\scriptsize my}\)Grid, MOBY-Services and Semantic-MOBY. Through an examination of the differences and similarities between the solutions produced, we highlight some of the practical difficulties in developing Semantic Web services and suggest that the experiences with these projects have implications for the development of Semantic Web services as a whole.


Service Provider Service Discovery Domain Ontology Service Description Service Interface 
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.
    Bada, M., Stevens, R., Goble, C., Gil, Y., Ashburner, M., Blake4, J.A., Cherry, J.M., Harris, M., Lewis, S.: A Short Study on the Success of the Gene Ontology. Accepted for publication in the Journal of Web Semantics (2004)Google Scholar
  2. 2.
    Chicurel, M.: Bioinformatics: bringing it all together. Nature 419, 751–757 (2002)Google Scholar
  3. 3.
    Fielding, R.T.: Architectural styles and the design of network-based software architectures. PhD thesis, University of California, Irvine (2000)Google Scholar
  4. 4.
    Goble, C.A., Stevens, R., Ng, G., Bechhofer, S., Paton, N.W., Baker, P.G., Peim, M., Brass, A.: Transparent Access to Multiple Bioinformatics Information Sources. IBM Systems Journal Special issue on deep computing for the life sciences 40(2), 532–552 (2001)Google Scholar
  5. 5.
    Heß, A., Kushmerick, N.: Learning to attach semantic metadata to web services. In: Fensel, D., Sycara, K., Mylopoulos, J. (eds.) ISWC 2003. LNCS, vol. 2870, pp. 258–273. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  6. 6.
    Karp, P.: A Strategy for Database Interoperation. Journal of Computational Biology 2(4), 573–586 (1995)CrossRefGoogle Scholar
  7. 7.
    Lord, P., Wroe, C., Stevens, R., Goble, C., Miles, S., Moreau, L., Decker, K., Payne, T., Papay, J.: Semantic and Personalised Service Discovery. In: Cheung, W.K., Ye, Y. (eds.) WI/IAT 2003 Workshop on Knowledge Grid and Grid Intelligence, Halifax, Canada, October 2003, pp. 100–107 (2003)Google Scholar
  8. 8.
    Mandell, D.J., McIlraith, S.A.: Adapting BPEL4WS for the Semantic Web: The Bottom-Up Approach to Web Service Interoperation. In: Fensel, D., Sycara, K., Mylopoulos, J. (eds.) ISWC 2003. LNCS, vol. 2870, pp. 227–241. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  9. 9.
    Miller, R.A.: Medical diagnostic decision support systems–past, present, and future: a threaded bibliography and brief commentary. J. Am. Med. Inform. Assoc. 1(1), 8–27 (1994)CrossRefGoogle Scholar
  10. 10.
    Oinn, T., Addis, M., Ferris, J., Marvin, D., Greenwood, M., Carver, T., Wipat, A., Li, P.: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics (2004) (accepted for publication)Google Scholar
  11. 11.
    Paolucci, M., Ankolekar, A., Srinivasan, N., Sycara, K.: The DAML-S Virtual Machine. In: Internaional Semantic Web Conference, pp. 290–305 (2003)Google Scholar
  12. 12.
    Stevens, R., Glover, K., Greenhalgh, C., Jennings, C., Pearce, S., Li, P., Radenkovic, M., Wipat, A.: Performing in silico Experiments on the Grid: A Users’ Perspective. In: Proc. UK e-Science programme All Hands Conference (2003)Google Scholar
  13. 13.
    Senger, M., Rice, P., Oinn, T.: Soaplab – a unified sesame door to analysis tools. In: Proc. UK e-Science programme All Hands Conference (2003)Google Scholar
  14. 14.
    Stein, L.: Creating a bioinformatics nation. Nature 417, 119–120 (2002)CrossRefGoogle Scholar
  15. 15.
    Stevens, R., Tipney, H.J., Wroe, C., Oinn, T., Senger, M., Goble, C.A., Lord, P., Brass, A., Tassabehji, M.: Exploring Williams-Beuren Syndrome using my Grid. In: Proceedings of 12th International Conference on Intelligent Systems in Molecular Biology (2004) (Accepted for Publication)Google Scholar
  16. 16.
    Stevens, R.D., Goble, C.A., Baker, P., Brass, A.: A Classification of Tasks in Bioinformatics. Bioinformatics 17(2), 180–188 (2001)CrossRefGoogle Scholar
  17. 17.
    Stevens, R.D., Robinson, A.J., Goble, C.A.: myGrid: personalised bioinformatics on the information grid. Bioinformatics 19(90001), 302i–304 (2003)CrossRefGoogle Scholar
  18. 18.
    Sycara, K., Paolucci, M., Ankolekar, A., Srinivasan, N.: Automated discovery, interaction and composition of semantic web services. Journal of Web Semantics 1(1), 27–46 (2003)Google Scholar
  19. 19.
    Vogels, W.: Web services are not distributed objects. IEEE Internet Computing 7(6), 59–66 (2003)CrossRefGoogle Scholar
  20. 20.
    Wilkinson, M.D., Gessler, D., Farmer, A., Stein, L.: The BioMOBY Project Explores Open-Source, Simple, Extensible Protocols for Enabling Biological Database Interoperability. Proc. Virt. Conf. Genom. and Bioinf. 3, 16–26 (2003)Google Scholar
  21. 21.
    Wilkinson, M.D., Links, M.: BioMOBY: an open-source biological web services proposal. Briefings In Bioinformatics 3(4), 331–341 (2002)CrossRefGoogle Scholar
  22. 22.
    Wroe, C., Goble, C., Greenwood, M., Lord, P., Miles, S., Papay, J., Payne, T., Moreau, L.: Automating experiments using semantic data on a bioinformatics grid. IEEE Intelligent Systems 19(1), 48–55 (2004)CrossRefGoogle Scholar
  23. 23.
    Wu, D., Parsia, B., Sirin, E., Hendler, J., Nau, D.: Automating DAML-S web services composition using SHOP2. In: Fensel, D., Sycara, K., Mylopoulos, J. (eds.) ISWC 2003. LNCS, vol. 2870, pp. 195–210. Springer, Heidelberg (2003)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Phillip Lord
    • 1
  • Sean Bechhofer
    • 1
  • Mark D. Wilkinson
    • 2
  • Gary Schiltz
    • 3
  • Damian Gessler
    • 3
  • Duncan Hull
    • 1
  • Carole Goble
    • 1
  • Lincoln Stein
    • 4
  1. 1.Department of Computer ScienceUniversity of ManchesterManchesterUK
  2. 2.James Hogg iCAPTURE Centre, St. Paul’s HospitalUniversity of British ColumbiaVancouverCanada
  3. 3.National Center for Genome ResourcesSanta FeUS
  4. 4.Cold Spring Harbor LaboratoryCold Spring HarborUS

Personalised recommendations