Skip to main content

Constructing a Domain-Specific DBMS using a Persistent Object System

  • Conference paper
Book cover Persistent Object Systems

Part of the book series: Workshops in Computing ((WORKSHOPS COMP.))

Abstract

Constructing a light-weight domain-specific database management system (DBMS) is one way “′to design applications that effectively exploit… persistent technology”. We have implemented a domain-specific DBMS, LabBase, on top of the ObjectStore persistent object system (which is basically a persistent C++). LabBase is tailored to the application domain of laboratory information systems: it is designed to record experimental steps and results in a high-throughput laboratory production line—for example, one of those operated as part of the Whitehead/MIT Genome Center’s genome-mapping projects.

This work was supported by funds from the U.S. National Institutes of Health, National Center for Human Genome Research, grant number P50 HG00098.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. C. Lamb, G. Landis, J. Orenstein, and D. Weinreb, “The ObjectStore database system,” Communications of the ACM, vol. 34, pp. 50–63, Oct. 1991.

    Article  Google Scholar 

  2. J. Orenstein, S. Haradhvala, B. Margulies, and D. Sakahara, “Query processing in the ObjectStore database system,” in Proceedings of the 1992 ACM SIGMOD International Conference on Management of Data (M. Stonebraker, ed.), pp. 403–412, June 1992.

    Google Scholar 

  3. Object Design, Inc., 25 Burlington Mall Rd., Burlington MA 01803-4194, USA, Manual set for ObjectStore Release 3.0 for UNIX Systems, Dec. 1993.

    Google Scholar 

  4. A. R. Kerlavage, M. D. Adams, J. C. Kelly, et al., “Analysis and management of data from high-throughput expressed sequence tag projects,” in Proceedings of the 26th Annual Hawaii International Conference on System Sciences (T. N. Mudge, V. Milutinovic, and L. Hunter, eds.), vol. 1, pp. 585–594, IEEE Computer Society Press, Jan. 1993.

    Google Scholar 

  5. S. P. Clark, G. A. Evans, and H. R. Garner, “Informatics and automation used in physical mapping of the genome,” in Biocomputing Informatics and Genome Projects (D. W. Smith, ed.), pp. 13–49, Academic Press, Inc., 1994.

    Google Scholar 

  6. L. Stein, A. Marquis, E. Dredge, et al., “Splicing UNIX into a genome mapping laboratory,” in USENIX Summer 1994 Technical Conference, pp. 221–229, June 1994.

    Google Scholar 

  7. C. Burks, M. Cassidy, M. J. Cinkosky, et al, “GenBank,” Nucleic Acids Research, pp. 2221–2225, 1991.

    Google Scholar 

  8. R. Durbin and J. Thierry-Mieg, “A C. elegans database,” 1991. Documentation, code and data available from anonymous ftp servers at lirmm. lirmm. fr, cele. mrc-lmb. cam.ac.uk and ncbi. nlm. nih. gov.

    Google Scholar 

  9. T. Berners-Lee, R. Cailliau, J.-F. Groff, and B. Pollermann, “World-Wide Web: The information universe,” Electronic Networking: Research, Applications and Policy, vol. 2, no. 1, pp. 52–58, 1992. Also available at http://info.cern.ch/hypertext/WWW/Bibliography/Papers.html.

    Article  Google Scholar 

  10. L. Wall and R. L. Schwartz, Programming perl O’Reilly & Associates, Inc., 1990.

    Google Scholar 

  11. N. Goodman, “An object oriented DBMS war story: Developing a genome mapping database in C++,” in Modern Database Management: Object-Oriented and Multidatabase Technologies (W. Kim, ed.), ACM Press, 1994.

    Google Scholar 

  12. N. Goodman, S. Rozen, and L. Stein, “Requirements for a deductive query language in the MapBase genome-mapping database,” in Applications of Deductive Databases (tentative) (R. Ramakrishnan, ed.), Kluwer, 1994. In press. Available at ftp://genome.wi.mit.edu/pub/papers/Y1994/requirements.ps.

  13. ONTOS, Inc., Three Burlington Woods, Burlington MA 01803, USA, ONTOS DB 2.2 Developer’s Guide, Feb. 1992.

    Google Scholar 

  14. Versant Object Technology Corporation, 4500 Bohannon Drive, Menlo Park CA 94025, USA, VERSANT Object Database Management System Release 2 System Manual, July 1993. Part Number 1003-0793.

    Google Scholar 

  15. S. Tsur, “Data dredging,” Data Engineering, vol. 13, Dec. 1990.

    Google Scholar 

  16. R. Ramakrishnan, D. Srivastava, and S. Sudarshan, “CORAL-control, relations and logic,” in Proceedings of the 18th International Conference on Very Large Data Bases (L.-Y. Yuan, ed.), pp. 238–250, Aug. 1992. A longer version is available from the authors.

    Google Scholar 

  17. S. Tsur and C. Zaniolo, “LDL: a logic-based data language,” in Proceedings of the 12th International Conference on Very Large Data Bases, pp. 33–41, Aug. 1986.

    Google Scholar 

  18. S. Rozen, L. Stein, and N. Goodman, LabBase User Manual Available at ftp://genome.wi.mit.edu/pub/papers/Y1994/labbase-manual.ps.

  19. P. O’Brien, “R3 & R4 product directions overview,” Mar. 1994. Talk presented at ObjectStore Northeast users group meeting.

    Google Scholar 

  20. T. Mason and D. Brown, lex & yac. O’Reilly & Associates, 1991.

    Google Scholar 

  21. L. Haas et al., Starburst mid-flight: As the dust clears,” IEEE Trans. on Knowledge and Data Eng., vol. 2, Mar. 1990.

    Google Scholar 

  22. M. Stonebraker, “Object-relational data base systems,” 1993. Distributed with Montage (now called Illustra) sales literature.

    Google Scholar 

  23. D. S. Batory, J. R. Barnett, J. F. Garza, et al., “GENESIS: An extensible database management system,” IEEE Trans. on Software Eng., vol. 14, pp. 1711–1730, Nov. 1988.

    Article  Google Scholar 

  24. D. Batory and S. O’Malley, “The design and implementation of hierarchical software systems with reusable components,” ACM Trans, on Software Engineering, vol. 1, Oct. 1992.

    Google Scholar 

  25. D. S. Batory, T. Y. Leung, and T. E. Wise, “Implementation concepts for an extensible data model and data language,” A CM Trans, on Database Syst, vol. 13, pp. 231–262, Sept. 1988.

    Article  Google Scholar 

  26. D. W. Shipman, “The functional data model and the data language DAPLEX,” ACM Trans. on Database Syst., vol. 6, no. 1, pp. 140–173, 1981.

    Article  Google Scholar 

  27. M. P. Atkinson, P. J. Bailey, K. J. Chisholm, W. P. Cockshott, and R. Morrison, “An approach to persistent programming,” The Computer Journal, vol. 26, no. 4, pp. 360–365, 1983.

    MATH  Google Scholar 

  28. K. G. Kulkarni and M. P. Atkinson, “Implementing an extended functional data model using PS-algol,” SoftwarePractice and Experience, vol. 17, pp. 171–183, Mar. 1987.

    Article  Google Scholar 

  29. W. Klas, K. Aberer, and E. Neuhold, “Object-oriented modeling for hypermedia systems using the VODAK Modelling Language (VML),” in Object-Oriented Database Management Systems, NATO ASI Series, Springer Verlag, Aug. 1993.

    Google Scholar 

  30. E. Neuhold. Personal communication, Sept. 15, 1994. Additional information, including VODAK source code, is available at http://este.darmstadt.gmd.de:5000/dimsys/home.html.

  31. O. Deux et al., “The O2 system,” Communications of the ACM, vol. 34, pp. 34–48, Oct. 1991.

    Article  Google Scholar 

  32. P. Butterworth, A. Otis, and J. Stein, “The GemStone object database management system,” Communications of the ACM, vol. 34, pp. 65–77, Oct. 1991.

    Article  Google Scholar 

  33. B. Liskov, M. Day, and L. Shrira, “Distributed object management in Thor,” in Distributed Object Management (T. Ozsu, U. Dayal, and P. Val-duriez, eds.), Morgan Kaufmann, 1994.

    Google Scholar 

  34. M. Day, R. Gruber, B. Liskov, and A. C. Myers, “Abstraction mechanisms in Theta,” 1994. Submitted for publication.

    Google Scholar 

  35. R. Morrison, A. L. Brown, R. C. H. Connor, et al., “The Napier88 reference manual (release 2.0),” Tech. Rep. CS/93/15, University of St. Andrews, 1993.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1995 British Computer Society

About this paper

Cite this paper

Rozen, S., Stein, L., Goodman, N. (1995). Constructing a Domain-Specific DBMS using a Persistent Object System. In: Atkinson, M., Maier, D., Benzaken, V. (eds) Persistent Object Systems. Workshops in Computing. Springer, London. https://doi.org/10.1007/978-1-4471-2122-0_41

Download citation

  • DOI: https://doi.org/10.1007/978-1-4471-2122-0_41

  • Publisher Name: Springer, London

  • Print ISBN: 978-3-540-19912-0

  • Online ISBN: 978-1-4471-2122-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics