Semantic Web pp 399-412 | Cite as

Factors Influencing the Adoption of the Semantic Web in the Life Sciences

  • Toni Kazic


The Semantic Web today is a vision of transparent search, request, manipulation, and delivery of information to the user by an interconnected set of services. This vision would change the way scientists interact with data, computations, and even each other. Realizing it begins with understanding the needs of biologists and the dynamic continuum of factors that will determine whether, in what form, and at what rate the Semantic Web is likely to be adopted as a scientific tool by this community. In this chapter I look at this continuum and hazard some predictions.

Key words

adaptability community cost fanfare fate of technology friction impetus need performance persistence support 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. [1]
    Altman R.B., Klein T.E., Murray T., and Dunker A.K., editors. Pacific Symposium on Biocomputing, 2006, Singapore, 2006. World Scientific Publishing Co.Google Scholar
  2. [2]
    Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M, Rubin G.M., and Sherlock G. Gene Ontology: tool for the unification of biology. Nature Genet., 25:25–29, 2000.PubMedCrossRefGoogle Scholar
  3. [3]
    Bader G.D. and Hogue C.W.V. BIND — a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics, 16:465–477, 2000.PubMedCrossRefGoogle Scholar
  4. [4]
    Beckett D., editor. RDF/XML Syntax Specification (Revised). W3C, 2004. Scholar
  5. [5]
    Berners-Lee T. Semantic Web Road Map, 1998. W3C, Scholar
  6. [6]
    BioPAX Group. BioPAX: Biological Pathways Exchange, 2002. Scholar
  7. [7]
    Brickley D. and Guha R.V., editors. RDF Vocabulary Description Language 1.0: RDF Schema, 2004. W3C, Scholar
  8. [8]
    Carroll J.J. and De Roo J., editors. OWL Web Ontology Language Test Cases. W3C, 2004. Scholar
  9. [9]
    Cerami E. Web Services Essentials. O’Reilly and Associates, Inc., Sebastopol CA, 2002.Google Scholar
  10. [10] eclipse, 2006. Scholar
  11. [11]
    Gene Ontology Consortium. 2003. Scholar
  12. [12]
    Gennari J., Musen M.A., Fergerson R.W., Grosso W.E., Crubezy M., Eriksson H., Noy N.F., and Tu S.W. The evolution of Protégé: an environment for knowledge-based systems development. Technical report, Stanford University SMI-2002=0943, 2002. Scholar
  13. [13]
    Globus Team. The Globus Project, 2003. Scholar
  14. [14]
    Harold E.R. and Means W.S. XML in a Nutshell. O’Reilly and Associates, Inc., Sebastopol CA, second edition, 2002.Google Scholar
  15. [15]
    Hayes P., editor. RDF Semantics. W3C, 2004. Scholar
  16. [16]
    Hucka M., Finney A., Bornstein B.J., Keating S.M., Shapiro B.E., Matthews J., Kovita B.L., Schilstra M.J., Funahashi A., Doyce J.C., and Kitano H. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Sys. Biol., 1:41–53, 2004.CrossRefGoogle Scholar
  17. [17]
    International Union of Biochemistry and Molecular Biology. Enzyme Nomenclature. Recommendations (1992) of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Academic Press, Inc., London, 1992.Google Scholar
  18. [18]
    Katz M.L. and Shapiro C. Network externalities, competition, and compatibility. Am. Econ. Rev., 75:424–440, 1985.Google Scholar
  19. [19]
    Katz M.L. and Shapiro C. Product introduction with network externalities. J. Ind. Econ., 40:55–83, 1992.CrossRefGoogle Scholar
  20. [20]
    Kazic T. Representation, reasoning and the intermediary metabolism of Escherichia coli. In Trevor N. Mudge, Veljko Milutinovic, and Lawrence Hunter, editors, Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, volume 1, pages 853–862, Los Alamitos CA, 1993. IEEE Computer Society Press.Google Scholar
  21. [21]
    Kazic T. Semiotes — a semantics for sharing. Bioinformatics, 16:1129–1144, 2000.PubMedCrossRefGoogle Scholar
  22. [22]
    Kazic T. Putting semantics into the Semantic Web: how well can it capture biology? In Klein T.E., Murray T., and Dunker A.K., editors. Pacific Symposium on Biocomputing, 2006, Singapore, 2006 Altman et al. [1], pages 140–151.Google Scholar
  23. [23]
    Lloyd C.M., Halstead M.D.B., and Nielsen P.F. CellML: its future, present, and past. Prog. Biophys. Mol. Biol., 85:433–450, 2004.PubMedCrossRefGoogle Scholar
  24. [24]
    Lutz C, editor. Description Logics, 2005. Scholar
  25. [25]
    MaizeGDB. MaizeGDB, 2003. Iowa State University, Scholar
  26. [26]
    McGuinness D.L. and van Harmelen F., editors. OWL Web Ontology Language Overview. W3C, 2004. Scholar
  27. [27]
    Microarray Gene Expression Data Society. MGED Home. Microarray Gene Expression Data Society, 2002. Scholar
  28. [28]
    National Center for Biomedical Ontology. OBO: open biomedical ontologies. National Center for Biomedical Ontology, 2005. Scholar
  29. [29]
    National Library of Medicine. National Library of Medicine Fact Sheet: UMLS Semantic Network. National Library of Medicine, 1999. Scholar
  30. [30]
    Neumann E.K. and Quan D. BioDASH: a Semantic Web dashboard for drug development. In Klein T.E., Murray T., and Dunker A.K., editors. Pacific Symposium on Biocomputing, 2006, Singapore, 2006 Altman et al. [1], pages 176–187.Google Scholar
  31. [31]
    Ostell J. NCBI ASN.1 specifications. 1990. Scholar
  32. [32]
    Patel-Schneider P.F. and Horrocks I., editors. OWL Web Ontology Language Semantics and Abstract Syntax, 2004. W3C, Scholar
  33. [33]
    Plant Ontology Consortium. Plant Ontology. Plant Ontology Consortium, 2003. Scholar
  34. [34]
    PredictProtein Team. PredictProtein. Columbia University, 2003. Scholar
  35. [35]
    Rosse C. and Mejino J.L.V. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Biomed. Inform., 36:478–500, 2003.PubMedCrossRefGoogle Scholar
  36. [36]
    Rost B., Yachdav G., and Liu J. The PredictProtein server. Nucleic Acids Res., 32:W321–W326, 2003.CrossRefGoogle Scholar
  37. [37]
    Sheth A.P. and Larson J.A. Federated database systems for managing distributed, heterogeneous, and autonomous databases. ACM Comp. Surv., 22:183–236, 1990.CrossRefGoogle Scholar
  38. [38]
    Snell J., Tidwell D., and Kulchenko P. Programming Web Services with SOAP. O’Reilly and Associates, Inc., Sebastopol CA, 2002.Google Scholar
  39. [39]
    Subramaniam S. The Biology Workbench: a seamless database and analysis environment for the biologist. Proteins, 32:1–2, 1998.PubMedCrossRefGoogle Scholar
  40. [40]
    Weinberg B.A. Experience and technology adoption. discussion paper no. 1051. Technical report, Institute for the Study of Labor (IZA), Bonn, 2004.Google Scholar
  41. [41]
    Wilshire Conferences. Semantic Technology Conference. In 2006 Semantic Technology Conference, 2006. Wilshire Conferences.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Toni Kazic
    • 1
  1. 1.Department of Computer ScienceUniversity of MissouriUSA

Personalised recommendations