e-Science and the Semantic Web: A Symbiotic Relationship

  • Carole Goble
  • Oscar Corcho
  • Pinar Alper
  • David De Roure
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4265)


e-Science is scientific investigation performed through distributed global collaborations between scientists and their resources, and the computing infrastructure that enables this. Scientific progress increasingly depends on pooling know-how and results; making connections between ideas, people, and data; and finding and reusing knowledge and resources generated by others in perhaps unintended ways. It is about harvesting and harnessing the “collective intelligence” of the scientific community. The Semantic Web is an extension of the current Web in which information is given well-defined meaning to facilitate sharing and reuse, better enabling computers and people to work in cooperation. Applying the Semantic Web paradigm to e-Science has the potential to bring significant benefits to scientific discovery. We identify the benefits of lightweight and heavyweight approaches, based on our experiences in the Life Sciences.


Gene Ontology Symbiotic Relationship Collective Intelligence Semantic Grid Global Grid Forum 
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.
    Hey, T., Trefethen, A.E.: Cyberinfrastructure for e-Science. Science 308(5723), 817–821 (2005)CrossRefGoogle Scholar
  2. 2.
    Stevens, R., et al.: Exploring Williams-Beuren Syndrome Using myGrid. In: 12th International Conference on Intelligent Systems in Molecular Biology. Bioinformatics, Glasgow (2004)Google Scholar
  3. 3.
    NAR1, Web Server issue. Nucleic Acids Research 34 (2006)Google Scholar
  4. 4.
    NAR2, Database Issue. Nucleic Acids Research 34 (2006)Google Scholar
  5. 5.
    Hey, A.J.G., Trefethen, A.E.: The Data Deluge: An e-Science Perspective. In: Berman, F., Fox, G.C., Hey, A.J.G. (eds.) Grid Computing - Making the Global Infrastructure a Reality, pp. 809–824. Wiley and Sons, Chichester (2003)Google Scholar
  6. 6.
    Szalay, A., Gray, J.: 2020 Computing: Science in an exponential world. Nature 440, 413–414 (2006)CrossRefGoogle Scholar
  7. 7.
    Berners-Lee, T., Hendler, J., Lassila, O.: The Semantic Web. Scientific American 284(5), 34–43 (2001)CrossRefGoogle Scholar
  8. 8.
    Hendler, J.: Science and the Semantic Web. Science 299, 520–521 (2003)CrossRefGoogle Scholar
  9. 9.
    Baker, C.J.O., Cheung, K.-H. (eds.): Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (in press, 2006)Google Scholar
  10. 10.
    Schroeder, M., Neumann, E.: Special Issue on Semantic Web in Life Sciences. Journal of Web Semantics 4(3) (2006)Google Scholar
  11. 11.
    Stevens, R., Bodenreider, O., Lussier, Y.A.: Semantic Webs for Life Sciences Session Introduction. In: Pacific Symposium on Biocomputing (2006)Google Scholar
  12. 12.
    Kazic, T.: Putting Semantics into the Semantic Web: How Well Can It Capture Biology? In: Pacific Symposium on Biocomputing (2006)Google Scholar
  13. 13.
    Neumann, E.: A Life Science Semantic Web: Are We There Yet? Sci. STKE (283) (2005)Google Scholar
  14. 14.
    Goble, C.A.: Using the Semantic Web for e-Science: Inspiration, Incubation, Irritation. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 1–3. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  15. 15.
    Greenberg, J.: Metadata and the World Wide Web. The encyclopedia of library and information science 72, 244–261 (2002)Google Scholar
  16. 16.
    Antoniou, G., van Harmelen, F.: A Semantic Web Primer. MIT Press, Cambridge (2004)Google Scholar
  17. 17.
    Oinn, T., et al.: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics Journal 20(17), 3045–3054 (2004)CrossRefGoogle Scholar
  18. 18.
    Garwood, K., Lord, P., Parkinson, H., Paton, N.W., Goble, C.A.: Pedro ontology services: A framework for rapid ontology markup. In: Gómez-Pérez, A., Euzenat, J. (eds.) ESWC 2005. LNCS, vol. 3532, pp. 578–591. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  19. 19.
    Frey, J.G., De Roure, D., Carr, L.A.: Publication At Source: Scientific Communication from a Publication Web to a Data Grid. In: Euroweb 2002 Conference, The Web and the GRID: from e-science to e-business. BCS, Oxford, UK (2002)Google Scholar
  20. 20.
    Taylor, K., et al.: A Semantic Datagrid for Combinatorial Chemistry. In: 6th IEEE/ACM International Workshop on Grid Computing, Seattle (2005)Google Scholar
  21. 21.
    Hughes, G., et al.: The Semantic Smart Laboratory: A system for supporting the chemical e-Scientist. Organic & Biomolecular Chemistry 2(22), 3284–3293 (2004)CrossRefGoogle Scholar
  22. 22.
    Bachler, M., et al.: Collaborative Tools in the Semantic Grid. In: GGF11 - The Eleventh Global Grid Forum. Global Grid Forum, Honolulu (2004)Google Scholar
  23. 23.
    Zhao, J., Wroe, C., Goble, C.A., Stevens, R., Quan, D., Greenwood, M.: Using Semantic Web Technologies for Representing E-science Provenance. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 92–106. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  24. 24.
    Frey, J., De Roure, D.C., Taylor, K., Essex, J., Mills, H., Zaluska, E.J.: CombeChem: A Case Study in Provenance and Annotation Using the Semantic Web. In: Moreau, L., Foster, I. (eds.) IPAW 2006. LNCS, vol. 4145, pp. 270–277. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  25. 25.
    Corcho, O., Fernández-López, M., Gómez-Pérez, A.: Methodologies, tools and languages for building ontologies. Where is their meeting point? Data & Knowledge Engineering 46(1), 41–64 (2003)CrossRefGoogle Scholar
  26. 26.
    O’Reilly, T.: What Is Web 2.0 (2005), [cited, July 2006]; Available from:
  27. 27.
    Gruber, T.: Ontology of Folksonomies: A Mash-up of Apples and Oranges (2005), [cited, July 2006]; Available from:
  28. 28.
    Corcho, O.: Ontology-based document annotation: trends and open research problems. International Journal of Metadata, Semantics and Ontologies 1(1), 47–57 (2006)CrossRefMathSciNetGoogle Scholar
  29. 29.
    Uren, V., et al.: Semantic Annotation for Knowledge Management: Requirements and a Survery of the State of the Art. Journal of Web Semantics 4(1) (2006)Google Scholar
  30. 30.
    Bizer, C.: D2R MAP – A DB to RDF Mapping Language. In: 12th International World Wide Web Conference (WWW 2003), Budapest, Hungary (2003)Google Scholar
  31. 31.
    Bergman, M.K.: The deep Web: surfacing hidden information. The Journal of Electronic Publishing 7(1) (2001)Google Scholar
  32. 32.
    Stephens, S., et al.: Aggregation of bioinformatics data using Semantic Web technology. Journal of Web Semantics 4(3) (2006)Google Scholar
  33. 33.
    Bourne, P.: Will a Biological Database Be Different from a Biological Journal? PLoS Comput. Biol. 1(3), e34 (2005)Google Scholar
  34. 34.
    Bechhofer, S., Stevens, R., Lord, P.: Ontology Driven Dynamic Linking of Biology Resources. In: Pacific Symposium on Biocomputing, Hawaii (2005)Google Scholar
  35. 35.
    Cheung, K.H., et al.: YeastHub: A semantic web use case for integrating data in the life sciences domain. Bioinformatics 21(1), i85–i96 (2005)Google Scholar
  36. 36.
    Taylor, K.R., et al.: Bringing Chemical Data onto the Semantic Web. J. Chem. Inf. Model. 46, 939–952 (2006)CrossRefGoogle Scholar
  37. 37.
    Myers, J.D., et al.: A Collaborative Informatics Infrastructure for Multi-scale Science. In: Second International Workshop on Challenges of Large Applications in Distributed Environments, Honolulu, Hawaii (2004)Google Scholar
  38. 38. news service and Translator lets computers “understand” experiments (2006), [cited, July 2006]; Available from:
  39. 39.
    Wang, X., Gorlitsky, R., Almeida, J.S.: From XML to RDF: How Semantic Web Technologies Will Change the Design of ‘Omic’ Standards. Nature Biotechnology 23(9), 1099–1103 (2005)CrossRefGoogle Scholar
  40. 40.
    Blake, J.: Bio-ontologies—fast and furious. Nature Biotechnology 22, 773–774 (2004)CrossRefGoogle Scholar
  41. 41.
    Cheung, K.-H., et al.: A semantic web approach to biological pathway data reasoning and integration. Journal of Web Semantics 4(3) (2006)Google Scholar
  42. 42.
    Lord, P., Alper, P., Wroe, C., Goble, C.A.: Feta: A light-weight architecture for user oriented semantic service discovery. In: Gómez-Pérez, A., Euzenat, J. (eds.) ESWC 2005. LNCS, vol. 3532, pp. 17–31. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  43. 43.
    Wroe, C.J., et al.: Methodology To Migrate The Gene Ontology To A Description Logic Environment Using DAML+OIL. In: 8th Pacific Symposium on Biocomputing (PSB), Hawaii (2003)Google Scholar
  44. 44.
    Stevens, R., et al.: Managing OWL’s Limitations in Modelling Biomedical Knowledge. Intl. Journal of Human Computer Systems (Accepted for publication)Google Scholar
  45. 45.
    Zhang, S., Bodenreider, O., Golbreich, C.: Experience in Reasoning with the Foundational Model of Anatomy in OWL DL. In: Pacific Symposium on Biocomputing (2006)Google Scholar
  46. 46.
    Neumann, E.K., Quan, D.: Biodash: A Semantic Web Dashboard for Drug Development. In: Pacific Symposium on Biocomputing (2006)Google Scholar
  47. 47.
    Gates, W.: Opening Keynote. In: SuperComputing 2005 (SC 2005). Seattle, Washington (2005)Google Scholar
  48. 48.
    Goble, C., Stevens, R., Bechhofer, S.: The Semantic Web and Knowledge Grids. Drug Discovery Today: Technologies 2(3), 193–302 (2005)CrossRefGoogle Scholar
  49. 49.
    Wolstencroft, K., Brass, A., Horrocks, I., Lord, P., Sattler, U., Turi, D., Stevens, R.: A Little Semantic Web Goes a Long Way in Biology. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 786–800. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  50. 50.
    W3C, Workshop on Semantic Web for Life Sciences. Cambridge, Massachusetts (2004)Google Scholar
  51. 51.
    Gao, Y., et al.: SWAN: A distributed knowledge infrastructure for Alzheimer disease research. Journal of Web Semantics 4(3) (2006)Google Scholar
  52. 52.
    Goble, C.A., De Roure, D.: The Semantic Grid: Building Bridges and Busting Myths. In: 16th European Conference in Artificial Intelligence (ECAI 2004), Valencia, Spain (2004)Google Scholar
  53. 53.
    De Roure, D., Jennings, N.R., Shadbolt, N.R.: The Semantic Grid: Past, Present, and Future. Proceedings of the IEEE 93(3), 669–681 (2005)CrossRefGoogle Scholar
  54. 54.
    Goble, C.A., et al.: Enhancing Services and Applications with Knowledge and Semantics. In: Foster, I., Kesselman, C. (eds.) The Grid 2: Blueprint for a New Computing Infrastructure, pp. 431–458. Morgan Kaufmann, San Francisco (2004)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Carole Goble
    • 1
  • Oscar Corcho
    • 1
  • Pinar Alper
    • 1
  • David De Roure
    • 2
  1. 1.School of Computer ScienceUniversity of ManchesterManchesterUK
  2. 2.School of Electronics and Computer ScienceUniversity of SouthamptonSouthamptonUK

Personalised recommendations