Using Semantic Web Technologies for Representing E-science Provenance

  • Jun Zhao
  • Chris Wroe
  • Carole Goble
  • Robert Stevens
  • Dennis Quan
  • Mark Greenwood
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3298)

Abstract

Life science researchers increasingly rely on the web as a primary source of data, forcing them to apply the same rigor to its use as to an experiment in the laboratory. The \({}^{\mbox{\scriptsize my}}\)Grid project is developing the use of workflows to explicitly capture web-based procedures, and provenance to describe how and why results were produced. Experience within \({}^{\mbox{\scriptsize my}}\)Grid has shown that this provenance metadata is formed from a complex web of heterogenous resources that impact on the production of a result. Therefore we have explored the use of Semantic Web technologies such as RDF, and ontologies to support its representation and used existing initiatives such as Jena and LSID, to generate and store such material. The effective presentation of complex RDF graphs is challenging. Haystack has been used to provide multiple views of provenance metadata that can be further annotated. This work therefore forms a case study showing how existing Semantic Web tools can effectively support the emerging requirements of life science research.

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References

  1. 1.
    Karp, P.: A Strategy for Database Interoperation. Journal of Computational Biology 2, 573–586 (1995)CrossRefGoogle Scholar
  2. 2.
    Program, H.G.: Genomics and its impact on science and society: A 2003 primer. Technical report, U.S. Department of Energy (2003)Google Scholar
  3. 3.
    Fox, G., Walker, D.: e-Science Gap Analysis. Technical report, Indiana University and Cardiff University, UK e-Science Center (2003)Google Scholar
  4. 4.
    Stevens, R., Robinson, A., Goble, C.: myGrid: Personalised Bioinformatics on the Information Grid. In: International Conference on Intelligent Systems in Molecular Biology (2003)Google Scholar
  5. 5.
    Preus, M.: The Williams Syndrome: Objective Definition and Diagnosis. Clinical Genetics 25, 422–428 (1984)CrossRefGoogle Scholar
  6. 6.
    Hendler, J.: Communication: Enhanced Science and the Semantic Web. Science 299, 520–521 (2003)CrossRefGoogle Scholar
  7. 7.
    Martin, S., Senger, M., Niemi, M.: Life Sciences Identifiers second revised submission. Technical report, I3C (2003)Google Scholar
  8. 8.
    Quan, D., Karger, D.R.: How to make a semantic web browser. In: Proc. of the Thirteenth International World Wide Web Conference (WWW 2004), pp. 255–265. ACM, New York (2004)Google Scholar
  9. 9.
    Horrocks, I., Patel-Schneider, P.F., van Harmelen, F.: From SHIQ and RDF to OWL: The making of a web ontology language. Journal of Web Semantics 1, 7–26 (2003)Google Scholar
  10. 10.
    Cline, M., Shigeta, R., Wheeler, R., Siani-Rose, M., Kulp, D., Loraine, A.: The effects of alternative splicing on transmembrane proteins in the mouse genome. In: Pacific Symposium on Biocomputing, vol. 9, pp. 17–28 (2004)Google Scholar
  11. 11.
    Christensen, E., Curbera, F., Meredith, G., Weerawarana, S.: Web Services Description Language (WSDL) 1.1, W3C Note (2001)Google Scholar
  12. 12.
    Wroe, C., Stevens, R., Goble, C., Roberts, A., Greenwood, M.: A Suite of DAML+OIL Ontologies to Describe Bioinformatics Web Services and Data. The International Journal of Cooperative Information Systems 12, 597–624 (2003)Google Scholar
  13. 13.
    Quan, D., Huynh, D., Karger, D.R.: Haystack: A platform for authoring end user semantic web applications. In: Fensel, D., Sycara, K., Mylopoulos, J. (eds.) ISWC 2003. LNCS, vol. 2870, pp. 738–753. Springer, Heidelberg (2003)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Jun Zhao
    • 1
  • Chris Wroe
    • 1
  • Carole Goble
    • 1
  • Robert Stevens
    • 1
  • Dennis Quan
    • 2
  • Mark Greenwood
    • 1
  1. 1.Department of Computer ScienceUniversity of ManchesterUnited Kingdom
  2. 2.IBM T. J. Watson Research CenterCambridgeUSA

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