Abstract
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.
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References
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)
Chicurel, M.: Bioinformatics: bringing it all together. Nature 419, 751–757 (2002)
Fielding, R.T.: Architectural styles and the design of network-based software architectures. PhD thesis, University of California, Irvine (2000)
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)
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)
Karp, P.: A Strategy for Database Interoperation. Journal of Computational Biology 2(4), 573–586 (1995)
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)
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)
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)
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)
Paolucci, M., Ankolekar, A., Srinivasan, N., Sycara, K.: The DAML-S Virtual Machine. In: Internaional Semantic Web Conference, pp. 290–305 (2003)
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)
Senger, M., Rice, P., Oinn, T.: Soaplab – a unified sesame door to analysis tools. In: Proc. UK e-Science programme All Hands Conference (2003)
Stein, L.: Creating a bioinformatics nation. Nature 417, 119–120 (2002)
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)
Stevens, R.D., Goble, C.A., Baker, P., Brass, A.: A Classification of Tasks in Bioinformatics. Bioinformatics 17(2), 180–188 (2001)
Stevens, R.D., Robinson, A.J., Goble, C.A.: myGrid: personalised bioinformatics on the information grid. Bioinformatics 19(90001), 302i–304 (2003)
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)
Vogels, W.: Web services are not distributed objects. IEEE Internet Computing 7(6), 59–66 (2003)
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)
Wilkinson, M.D., Links, M.: BioMOBY: an open-source biological web services proposal. Briefings In Bioinformatics 3(4), 331–341 (2002)
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)
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)
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Lord, P. et al. (2004). Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds) The Semantic Web – ISWC 2004. ISWC 2004. Lecture Notes in Computer Science, vol 3298. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30475-3_25
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DOI: https://doi.org/10.1007/978-3-540-30475-3_25
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