A NEW GENERATION OF DIGITAL LIBRARY TO SUPPORT DRUG DISCOVERY RESEARCH

Edy S. Liongosari, Anatole V. Gershman, Mitu Singh

2004

Abstract

The recent explosion of publicly available biomedical information gave drug discovery researchers unprecedented access to a wide variety of online repositories, but the sheer volume of the available data diminishes its utility. This is compounded by the fact that these repositories suffer from a silo effect: data from one cannot be easily linked to data in another. This is true for both publicly available sources and internal sources such as project reports. The ability to explore all aspects of biological data and to link data across sources is beneficial, as it allows researchers to discover new knowledge and to identify new collaboration opportunities by exploiting links. This paper presents an approach to solving this problem and an application that allows researchers to browse and analyze disparate bio-medical repositories as one semantically integrated knowledge space.

References

  1. Ardley, H. C., Moynihan, T.P., Markham A.F. & Robinson P.A., 2000. 'Promoter analysis of the human ubiquitin-conjugating enzyme gene family UBE1LI-4, including UBE2L3 which encodes UbcH778, Biochim Biophys Acta, vol. 1491, no. 1-3, pp. 57-64.
  2. Brody, A.B., Dempski, K.L., Kaplan, J.E., Kurth, S.W., Liongosari, E.S. & Swaminathan, K. S., 1999. 'Integrating Disparate Knowledge Sources', Proc. Second Int. Conf. on Practical Application of Knowledge Management, pp. 77-82.
  3. Cohen, W.W., 2000. 'Data integration using similarity joins and a word-based information representation language', ACM Trans. Info. Systems, vol. 18, no. 3, pp. 288-321.
  4. Elmasri, R. & Navathe, S., 1999. 'Genome Data Management', in Fundamentals of Database Systems, Pearson Addison Wesley, 3rd edition, pp. 898-905.
  5. Etzold, T., Ulyanov A. & Argos, P., 1996. 'SRS: information retrieval system for molecular biology data banks', Methods in Enzymology, vol. 226, pp. 114-128.
  6. Fasulo, D., 1999. Analysis on recent work on clustering algorithms, Technical Report #01-03-02, Dept. of Computer Science and Eng., U of Washington, Seattle.
  7. Fayyad, U., Piatetsky-Shapiro, G. & Smyth, P., 1996. 'The KDD Process for Extracting Useful Knowledge from Volumes of Data', Comm. ACM, vol. 39, no. 11 pp. 27-34.
  8. Geffner, S., Agrawal, D., El Abbadi, A., & Smith, T., 1999. 'Browsing large digital library collections using classification hierarchies', Proc. Eighth Int. Conf. on Info. and Knowledge Management, pp. 195-201.
  9. Haas, L., Schwarz, P., Kodali, P., Kotlar, E., Rice, J. & Swope, W., 2001. 'DiscoveryLink: A system for integrated access to life sciences data sources', IBM Systems Journal, vol. 40, no. 2, pp. 489-511.
  10. Jacquemin, C., 2001. Spotting and discovering terms through NLP, MIT Press, Cambridge, MA.
  11. Katcher, B.S., 1999. MEDLINE: A Guide to Effective Searching, Ashbury Press, San Francisco, CA.
  12. Lambrix, P. & Jakoniene, V., 2003. 'Towards transparent access to multiple biological databanks', Proc. First Asia-Pacific Bioinformatics Conf., vol. 19, pp. 53-60.
  13. Lenzerini, M., 2002. 'Data Integration: A Theoretical Perspective', Proc. 21st ACM Symp. on Principles of Database Systems, pp. 233 - 246.
  14. Lowe, H. & Barnett, G., 1994. 'Understanding and using the medical subject headings (MESH) vocabulary to perform literature searchers', JAMA, vol. 271, pp. 1103-1108.
  15. National Library of Medicine, 2003 (updated 7 Feb 2003). Growth of GenBank. Retrieved 28 Jan 2004 from http://www.ncbi.nlm.nih.gov/Genbank/ genbankstats.html
  16. Schneiderman, B., 2000. 'Creating Creativity: User Interfaces for Supporting Innovation', ACM Trans. On Computer-Human Inter., vol. 7, no. 1, pp. 114-138.
  17. Wang M., Suzuki, T., Kitadata, T., Asakawa, S., Minoshima, S., Shimizu, N., Tanaka, K., Mizuno, Y. & Hattori, N., 2001. 'Developmental changes in the expression of parkin and UbcR7, a parkin-interacting and ubiquitin-conjugating enzyme, in rat brain', J. Neurochemistry, vol. 77, no. 6, pp. 1561-1568.
Download


Paper Citation


in Harvard Style

S. Liongosari E., V. Gershman A. and Singh M. (2004). A NEW GENERATION OF DIGITAL LIBRARY TO SUPPORT DRUG DISCOVERY RESEARCH . In Proceedings of the Sixth International Conference on Enterprise Information Systems - Volume 1: PRIS, (ICEIS 2004) ISBN 972-8865-00-7, pages 301-306. DOI: 10.5220/0002683603010306


in Bibtex Style

@conference{pris04,
author={Edy S. Liongosari and Anatole V. Gershman and Mitu Singh},
title={A NEW GENERATION OF DIGITAL LIBRARY TO SUPPORT DRUG DISCOVERY RESEARCH},
booktitle={Proceedings of the Sixth International Conference on Enterprise Information Systems - Volume 1: PRIS, (ICEIS 2004)},
year={2004},
pages={301-306},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002683603010306},
isbn={972-8865-00-7},
}


in EndNote Style

TY - CONF
JO - Proceedings of the Sixth International Conference on Enterprise Information Systems - Volume 1: PRIS, (ICEIS 2004)
TI - A NEW GENERATION OF DIGITAL LIBRARY TO SUPPORT DRUG DISCOVERY RESEARCH
SN - 972-8865-00-7
AU - S. Liongosari E.
AU - V. Gershman A.
AU - Singh M.
PY - 2004
SP - 301
EP - 306
DO - 10.5220/0002683603010306