Distributed and Parallel Databases

, Volume 1, Issue 3, pp 303–327 | Cite as

An approach for building an integrated environment for molecular biology databases

  • Nabil N. Kamel
  • Tao Song
  • Magdi Kamel
Article

Abstract

The requirements of a traditional integration of databases include hiding the heterogeneity among its member databases, preserving their autonomy, supporting controlled data sharing, and providing a user-friendly interface, with a performance comparable to that of a homogeneous distributed database system. In this paper, we describe a variation of the loosely coupled federated database approach that satisfies these requirements and is specifically oriented toward the special characteristics and needs of molecular biology databases. The approach differs from the traditional federated database approach in that it also integrates software tools together with the databases. In addition, the system gives the graphical user interface a more central role in the integration. Thus, the system has all the advantages provided by a visual user environment and is thus more user-friendly than traditional linguistic approaches. The paper also includes a description of XBio, a system which constructs such an integration. The design of XBio ensures robustness and can be customized to the needs of different classes of users.

Keywords

Molecular biology database integration federated databases graphical user interfaces 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    S.F. Altschul et al., “A basic alignment search tool,”J. Mol. Biol., vol. 215, p. 403, 1990.Google Scholar
  2. 2.
    H.S. Bilofsky et al., “The GenBank genetic sequence databank,”Nucleic Acid Res., vol. 14, pp. 1–17, 1985.Google Scholar
  3. 3.
    J. Devereux, P. Haeberli, and O. Smithies, “A comprehensive set of sequence analysis programs for the VAX,”Nucleic Acid Res. vol. 12, p. 387, 1984.PubMedGoogle Scholar
  4. 4.
    C.J. Gartmann and U. Grob, “A menu-shell for the GCG programs,”CABIOS, vol. 7, no. 4, 1991.Google Scholar
  5. 5.
    G.H. Gonnet and F.W. Tompa, “Mind your grammar: a new approach to modeling text,”Proc. 13th VLDB Conf., Brighton, England, 1987, pp. 339–346.Google Scholar
  6. 6.
    K. Hammer and D. Mcleod, “On database management system architecture,”Tech. Reports, MIT/LCS/TM-141, 1979.Google Scholar
  7. 7.
    N.N. Kamel, “A profile for molecular biology databases,”Comput. Appl. BOsci. Google Scholar
  8. 8.
    N.N. Kamel and M. Kamel, “Federated database management system: requirements, issues, and solutions,”Computer Communications, vol. 15, no. 6, pp. 270–278, 1992.Google Scholar
  9. 9.
    N.N. Kamel, T. Song, and M. Kamel, “Incorporating GUI in integration of molecular biology databases,”Third IEEE Workshop Future Trends Distributed Computing Systems in the 1990's, 1992.Google Scholar
  10. 10.
    W. Litwin and A. Abdellatif, “Multi-database interoperability,”IEEE Comput., vol. 19, no. 12, 1986.Google Scholar
  11. 11.
    W. Litwin, L. Mark, and N. Roussopoulos, “Interoperability of multiple autonomous databases,”ACM Comput. Surveys, vol. 22, no. 3, 1986.Google Scholar
  12. 12.
    Open Software Foundation, OSF/Motif R 1.1 series, Prentice Hall, 1991.Google Scholar
  13. 13.
    R.W. Scheifler and J. Gettys, “The X window system,”ACM Trans. Graph. vol. 5, no. 2, 1986.Google Scholar
  14. 14.
    A.P. Sheth and J.A. Larson, “Federated database systems for managing distributed, heterogeneous, and autonomous databases,”ACM Comput. Surveys, vol. 22, no. 3, 1990.Google Scholar

Copyright information

© Kluwer Academic Publishers 1993

Authors and Affiliations

  • Nabil N. Kamel
    • 1
  • Tao Song
    • 1
  • Magdi Kamel
    • 2
  1. 1.Database Systems Research and Development Center, Computer and Information SciencesUniversity of FloridaGainesville
  2. 2.Department of Information SystemsNaval Postgraduate SchoolMonterey

Personalised recommendations