Using Ontology with Semantic Web Services to Support Modeling in Systems Biology

  • Zhouyang Sun
  • Anthony Finkelstein
  • Jonathan Ashmore
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4832)


Modeling in systems biology is concerned with using experimental information and mathematical methods to build quantitative models at different biological scales. This requires interoperation among various knowledge sources and services, such as biological databases, mathematical equations, data analysis tools, and so on. Semantic Web Services provide an infrastructure that allows a consistent representation of these knowledge sources as web-based information units, and enables discovery, composition, and execution of these units by associating machine-processable semantics description with them. In this paper, we show a method of using ontology alongside a semantic web services infrastructure to provide a knowledge standardisation framework in order to support modeling in systems biology. We demonstrate how ontologies are used to control the transformation of biological databases and data analysis methods into Web Services, and how ontology-based web services descriptions (OWL-S), are used to enable the composition between these services.


Ontology OWL Semantic Web Services OWL-S Java EE 


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  1. 1.
    Finkelstein, A., et al.: Computational Challenges of Systems Biology. IEEE Computer 37(5), 26–33 (2004)MathSciNetGoogle Scholar
  2. 2.
    Noy, N.F., McGuinness, D.L.: Ontology Development 101: A Guide to Creating Your First Ontology - what is an ontology and why we need it,
  3. 3.
    Baker, C.J.O., Cheung, K.-H.: Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, 1st edn., Springer Science and Business Media, LLC (2007)Google Scholar
  4. 4.
    Berners-Lee: Semantic Web on XML - Keynote presentation for XML 2000,
  5. 5.
    Hudspeth, A.J., Lewis, R.S.: Kinetic Analysis of Voltage and Ion-dependent Conductances in Saccular Hair Cells of the Bull-frog, Rana Catesbeiana. J. Physiol. 400, 237–274 (1998)Google Scholar
  6. 6.
    Hodgkin, A.L., Huxley, A.F.: A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve. J. Physiol. 117, 500–544 (1952)Google Scholar
  7. 7.
  8. 8.
  9. 9.
  10. 10.
  11. 11.
  12. 12.
  13. 13.
  14. 14.
  15. 15.
  16. 16.
  17. 17.
  18. 18.
  19. 19.
  20. 20.
  21. 21.
    Uhrmacher, A.M., et al.: Towards Reusing Model Component in Systems Biology. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 192–206. Springer, Heidelberg (2005)Google Scholar
  22. 22.
    Nucleic Acids Research,
  23. 23.
  24. 24.
    myGrid and Taverna services,

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Zhouyang Sun
    • 1
  • Anthony Finkelstein
    • 1
  • Jonathan Ashmore
    • 1
  1. 1.CoMPLEX, University College London, WC1E 6BT, London 

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