Exploring heterogeneous biological databases: Tools and applications

  • Anthony S. Kosky
  • I -Min A. Chen
  • Victor M. Markowitz
  • Ernest Szeto
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1377)


We present a tool-based strategy for exploring heterogeneous biological databases in the context of the Object-Protocol Model (OPM). Our strategy involves tools for examining the semantics of biological databases; constructing and maintaining OPM views for biological databases; assembling biological databases into an OPM-based multidatabase system, while documenting database schemas and known links between databases; supporting multidatabase queries via uniform OPM interfaces; and assisting scientists in specifying and interpreting multidatabase queries. We describe these tools and discuss some of their scientific applications.


Query Language Biological Database Flat File Common Data Model Query Tree 
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.


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  1. 1.
    Buneman, P., Davidson, S., Hart, K., Overton, C, and Wong, L., A Data Transformation System for Biological Data Sources. In Proc. of the 21st Int. Conference on Very Large Data Bases, pp. 158–169, 1995.Google Scholar
  2. 2.
    Buneman, P., Naqvi, S., Tannen, V., Wong, L., Principles of Programming with Complex Objects and Collection Types. In Theoretical Computer Science 149, pp 3–48, 1995.CrossRefMathSciNetGoogle Scholar
  3. 3.
    Chen, I.A., and Markowitz, V.M., An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools. Information Systems, 20(5), pp. 393–418, 1995.CrossRefGoogle Scholar
  4. 4.
    Chen, I.A., and Markowitz, V.M., OPM Schema Translator 4, Reference Manual, Technical Report LBL-35582, 1996.Google Scholar
  5. 5.
    Chen, I.A., Kosky, A., Markowitz, V.M., and Szeto, E., The OPM Query Translator, Technical Report LBL-33706, 1996.Google Scholar
  6. 6.
    Chen, I.A., Kosky, A.S., Markowitz, V.M., and Szeto, E., Constructing and Maintaining Scientific Database Views, Proc. of the 9th Conference on Scientific and Statistical Database Management, IEEE Computer Society, pp. 237–248, 1997.Google Scholar
  7. 7.
    Etzold, T., and Argos, P., SRS, An Indexing and Retrieval Tools for Flat File Data Libraries. Computer Applications of Biosciences, 9, 1, pp. 49–57, 1993. See also Scholar
  8. 8.
    Fasman, K.H., Letovsky, S.I., Cottingham, R.W., and Kingsbury, D.T., Improvements to the GDB Human Genome Data Base. Nucleic Acids Research, Vol. 24, No. 1, pp. 57–63, 1996. See also Scholar
  9. 9.
    Markowitz, V.M., Chen, I.A., Kosky, A.S., and Szeto, E., Facilities for Exploring Molecular Biology Databases on the Web: A Comparative Study. Pacific Symposium on Biocomputing'97, Altman, R.B. & al (eds) World Scientific, 1997.Google Scholar
  10. 10.
    The Object Database Standard: ODMG-93, Cattell, R. G. G. (ed), Morgan Kaufmann, 1996.Google Scholar
  11. 11.
    Programmer's Reference. National Center for Biotechnology Information, Bethesda, Maryland, November 1991. See also the ASN.1 homepage at Scholar
  12. 12.
    Ritter, O. The Integrated Genomic Database. In Computational Methods in Genome Research (S. Suhai, ed.), pp. 57–73, Plenum, 1994.Google Scholar
  13. 13.
    Sheth, A.P., and Larson, J.A. Federated Database Systems for Managing Distributed, Heterogeneous, and Autonomous Databases. ACM Computing Surveys, 22(3), pp. 183–236, 1990.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1998

Authors and Affiliations

  • Anthony S. Kosky
    • 1
  • I -Min A. Chen
    • 1
  • Victor M. Markowitz
    • 1
  • Ernest Szeto
    • 1
  1. 1.Bioinformatics Systems DivisionGene Logic Inc.Berkeley

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