On the efficient evaluation of relaxed queries in biological databases

International Conference on Information and Knowledge Management, Proceedings

Volumn , Issue , 2002, Pages 227-236

  Chen, Yangjun ^a   Che, Duren ^b   Aberer, Karl ^c  

^a UNIVERSITY OF WINNIPEG   (Canada)

^b SOUTHERN ILLINOIS UNIVERSITY EDWARDSVILLE   (United States)

^c EPFL   (Switzerland)

Author keywords

Automation; Biological databases; Position trees; Query optimization; Query relaxation

Indexed keywords

ALGORITHMS; AUTOMATA THEORY; EQUIVALENCE CLASSES; FUZZY SETS; QUERY LANGUAGES;

BIOLOGICAL DATABASES; QUERY OPTIMIZATION; QUERY RELAXATION;

INFORMATION RETRIEVAL;

EID: 0037481038     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/584792.584832     Document Type: Conference Paper

References (32)

1. Ashburner, M., Ball, C.A., Black, J.A. and so on, Gene Ontology: tool for the unification of biology, Nature Genetics, Vol. 25, 2000, pp. 25-29.
2. Aho, A.V., Hopcroft, J.E. and Ullman, J.D., The Design and Analysis of Computer Algorithms, Addison-Wesley Publishing Com., London, 1969.
3. Aguilar, D., Oliva, B., Aviles, F.X. and Querol, E., TranScount: prediction of gene expression regulatory proteins from their sequences, Bioinformatics, Vol. 18, no. 4, 2002, pp. 597-607.
4. Brajnik, G., Mizzaro, S., Rasso, C., Evaluating User Interfaces to Information Retrieval Systems: A Case Study on User Support, in Proc. of the 19th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval (1996), pp. 128-136.
5. Coverson, C., Query Expansion Using and Interactive Concept Hierarchy, Master's dissertation, Department of Information Studies, University of Sheffield, 2000.
6. Cottawald, S., Fuzzy Sets and Fuzzy Logic: the foundations of application - from a mathematical point of view. Braunschweig, Wiesbaden: Vieweg, 1993.
7. Crochemore, M. and Rytter, W., Text Algorithms. Oxford University Press, New York, 1994.
8. Efthimiadis, E.N., Interactive Query Expansion: A user-nased evaluation in a relevance feedback environment, Journal of the American Society for Information Science, 51(11):989-1003, 2000.
9. GCRDb, URL: http://www.gcrdb.uthscsa.edu/.
10. Giancarlo, R. and Mignosi, F., Generalization of the periodicity theorem of Fine and Wilf, in Proc. CAAP 94, Lecture Notes in Computer Science, vol. 78, Springer, Berlin, 1994, pp. 130-141.
11. GPCR mutant database, URL: http://mgddk1.nid-dk.nih.gov:8000/GOCR.html.
12. GPCRDB, URL: http://www.sander.embl-heidelberg.de/7tm/.
13. Gonnet, G.H., Baeza-Yates, R.A. and Snider, T. New Indices for Text: PAT trees and PAT arrays, Information Retrieval, ed.: Frakes, W.B., Baeza-Yates, R.A., Prentice Hall, New Jersey, 1992, pp. 66-83.
14. Hopcroft, J.E. and Ullman, J.D., Formal Language and Their Relation to Automata, Addison-Wesley Publishing Com., London, 1969.
15. Knuth, D.E., The Art of Computer Programming: Sorting and Searching, Addison-Wesley Publishing Com., London, 1973.
16. Informix-Universal Server - Informix Guide to SQL, Informix Press, Menlo Park, CA, USA, 1997.
17. Kekakainen, J. and Jarvelin, K., The impact of query structure and query expansion on retrieval performance, In: Proc. of the 21th Annual International ACM SIGIR Conf. on Research and Development in Information Retrieval, Melbourne, Australia, August 23-28, 1998.
18. Jarvelin, K., Kristensen, J., Niemi, T., Sormunen, E., and Keskustalo, H., A deductive data model for query expansion, In: Proc. of the 19th Annual International ACM SIGIR Conf. on Research and Development in Information Retrieval, Zurich, Switzerland, 1996, pp. 235-243.
19. E.M. McCreight, "A space-economical suffix tree construction algorithm," J. ACM, Vol. 23, No. 2, 1976, pp. 262-272.
20. Morrison, D.R., PATRICIA - Practical Algorith To Retrieve Information Coded in Alphanumeric. Journal of Association for Computing Machinary, Vol. 15, No. 4, Oct. 1968, pp. 514-534.
21. U. Manber and E. Myers, "Suffix arrays: a new method for on-line string searches," SIAM J. Comput. 22 (Oct 1993), pp. 935-948.
22. Mitra, M., Singhal, A., and Buckley, C. Improving Automatic Query Expansion. In Proceedings of the 21st Annual International ACM-SIGIR, 1998, pp. 204-214.
23. National Center for Biotechnology Information. ENTREZ: Sequences User's Guide. National Library of Medicine, Bethesda, MD, 1992, Release 1.0.
24. Nucleic Acid Database Project (NDB), URL: http://ndb-server.rutgers.edu/NDB/structure-finder/tutorials, 2002.
25. Pearson, P., Matheson, N., Flescher, N., and Robbins, R.J., The GDB huan genome data base anno 1992. Nucleic Acids Research 20 (1992), 2201-2206.
26. SWISS-PROT Protein knowledgebase, URL: http://www.expasy.ch/sprot, 2002.
27. R. Tarjan, Depth-first Search and Linear Graph Algorithm, SIAM J. Comput. Vol. 1, No. 2, June 1972.
28. E. Ukkonen, "Constructing suffix trees on-line in linear time," in Proc. of IFIP'92, pp. 484-492.
29. Weiner P., Linear Pattern Matching Algorithms. Conf. Recorder, IEEE 14th Annual Symposium on Switching and Automata Theory, 1973, pp. 1-11.
30. The Protein Data Bank Through Microsoft Windows, URL: http://www.sdsc.edu/pb/wpdb/wpdb.htm, 2002.
31. Williams, H. and Zobel J., Indexing Nucleotide Databases for Fast Query Evaluation, in Proc. of 5th Int. Conf. on Extending Database Technology, Avignon, France, March 1998, pp. 275-288.
32. Yoon, J. and Kim, S.-H.A., Three-Level User Interface of Multimedia Digital Libraries with Relaxation and Restriction, in Proc. of IEEE International Forum on Research and Technology Advances in Digital Libraries (ADL'98), April 22-24, 1998, Santa Barbara, California, pp. 206-215.