Skip to main content

Realization of Biological Data Management by Object Deputy Database System

  • Conference paper
Transactions on Computational Systems Biology V

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 4070))

Abstract

Traditional database system is not suitable for biological data management. In this paper, we discuss how to manage a large amount of complex biological data by an object deputy database system which can provide rich semantics and enough flexibility. In our system, the flexible inheritance avoids a lot of data redundancy. Our cross class query mechanism allows users to find the more related data based on complex relationships. In addition, the schema evolution of biological data and their annotation can be easily supported along with biological knowledge accumulation. The experiment shows our approach is feasible and more efficient than the traditional ones.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. An allele frequency database for diverse populations and dna polymorphisms data structure in alfred. The Board of Regents of the University of Wisconsin System

    Google Scholar 

  2. Bairoch, A., Apweiler, R.: The swiss-prot protein sequence database and its supplement trembl in 2000. Nucleic Acids Res. 28(1), 45–48 (2000)

    Article  Google Scholar 

  3. Baker, W., van den Broek, A., Camon, E., Hingamp, P., Sterk, P., Stoesser, G., Tuli, M.: The EMBL Nucleotide Sequence Database (2000)

    Google Scholar 

  4. Barker, W.C., Garavelli, J.S., Huang, H., McGarvey, P.B., Orcutt, B.C., et al.: The protein information resource(pir). In: Nucleic Acids research 2000, vol. 28(1), pp. 41–44. Oxford University Press, Oxford (2000)

    Google Scholar 

  5. Benson, D., Karsch-Mizrachi, I., Lipman, D., Ostell, J., Rapp, B., Wheeler, D.: Genebank (2000)

    Google Scholar 

  6. Bry, F., Kroger, P.: A computational biology database digest: Data, data analysis, and data management. In: Distributed and Parallel Databases, pp. 7–42. Kluwer Academic Publishers Hingham, Dordrecht (2003)

    Google Scholar 

  7. Cattell, R.: The Object Database Standard:ODMG-93 (Release 1.1). Morgan Kaufmann, San Francisco (1994)

    Google Scholar 

  8. Chen, I.-M., Markowitz, V.: An overview of the object protocol model(opm) and the opm data management tools. In: Information Systems, 398-418 (1995)

    Google Scholar 

  9. Codd, E.F.: A relational model of data for large shared data banks. Communication of the ACM 13(6), 377–387 (1970)

    Article  MATH  Google Scholar 

  10. El-Sharkawi, M.E., Kambayashi, Y.: Object migration mechanisms to support object-oriented databases. In: Databases: Theory, Design, and Application, pp. 73–91 (1991)

    Google Scholar 

  11. Greer, D.S.: Pdbase: A relational database expression of macromolecular structure data

    Google Scholar 

  12. Gupta, A.: Life science research and data management c what can they give each other? In: ACM SIGMOD 2004 Electronic Proceedings, Paris, France, pp. 12–14. ACM, New York (2004)

    Google Scholar 

  13. Harger, C., Skupski, M., Bingham, J., Farmer, A., Hoisie, S.: The Genome Sequence DataBase(GSDB): improving data quality and data access (1998)

    Google Scholar 

  14. Heiler, S., Zdonick, S.: Object views: Extending the vision. In: Proc. of IEEE Sixth Int. Conf. On Data Engineering, pp. 86–93 (1990)

    Google Scholar 

  15. Hicks, M.G., Kettner, C.: Amaze:a database of molecular function,interactions and biochemical processes. In: Proceedings of the Beilstein-Institute Workshop (May 2002)

    Google Scholar 

  16. Huang, H., Barker, W.C., Chen, Y., Wu, C.H.: Iproclass: an integrated database of protein family classification, function and structure information. In: Nucleic Acids Research 2003, vol. 31, pp. 390–392. Oxford University Press, Oxford (2003)

    Google Scholar 

  17. Keet, C.M.M.: Biological data and conceptual modelling methods. Journal of Conceptual Modeling (October 2003)

    Google Scholar 

  18. Kim, W.: Object-oriented database systems: Promises, reality, and future. In: Proc. of the 19th VLDB, pp. 676–687 (1993)

    Google Scholar 

  19. Letovsky, S., Cottingham, R., Porter, C., Li, P.: GDB: the Human Genome Database (1998)

    Google Scholar 

  20. Baran, M.C., Moseley, H.N., Sahota, G., Montelione, G.T.: Spins: standardized protein nmr storage. a data dictionary and object-oriented relational database for archiving protein nmr spectra (October 2002)

    Google Scholar 

  21. Meyer, F., et al.: GenDB an open source genome annotation system for prokaryote genomes (2003)

    Google Scholar 

  22. Mieg, J.T., Mieg, D.T., Stein, L.: Acedb: A genome database management system. In: Computing in Science and Engineering, May/June 1999, vol. 1(3), pp. 44–52 (1999)

    Google Scholar 

  23. Paton, N.W., Khan, S.A., Hayes, A.: conceptual modeling of genomic information. In: Bioinformatics, June 2000, pp. 548–557 (2000)

    Google Scholar 

  24. Peng, Z.: An Object Deputy Model for Advanced Database Application. PhD Thesis, Kyoto University, Japan (1994)

    Google Scholar 

  25. Peng, Z., Kambayashi, Y.: Deputy mechanisms for object-oriented databases. In: Proceedings of the IEEE 11th Int. Conf. of Data Engineering, pp. 333–340 (1995)

    Google Scholar 

  26. Richardson, J., Schwariz, P.: Aspects:extending objects to support multiple, independent roles. In: Proc. of the Int. Conference on Management of Data, pp. 298–307 (1991)

    Google Scholar 

  27. Tateno, Y., Miyazaki, S., Ota, M., Sugawara, H., Gojobori, T.: DNA Data Bank of Japan (DDBJ) in Collaboration with Mass Sequencing Teams (2000)

    Google Scholar 

  28. Zhai, B., Shi, Y., Peng, Z.: Object deputy database language. In: The Fourth International Conference on Creating, Connecting and Collaborating through Computing (C5 2006) (January 2006)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Peng, Z., Shi, Y., Zhai, B. (2006). Realization of Biological Data Management by Object Deputy Database System. In: Priami, C., Hu, X., Pan, Y., Lin, T.Y. (eds) Transactions on Computational Systems Biology V. Lecture Notes in Computer Science(), vol 4070. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11790105_5

Download citation

  • DOI: https://doi.org/10.1007/11790105_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-36048-3

  • Online ISBN: 978-3-540-36049-0

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics