Optimized seamless integration of biomolecular data

Proceedings - 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering, BIBE 2001

Volumn , Issue , 2001, Pages 23-32

  Eckman, B A ^a,b   Lacroix, Z ^c   Raschid, L ^d  

^a GLAXOSMITHKLINE   (United States)

^b IBM   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COSTS; DECISION SUPPORT SYSTEMS; DIGITAL LIBRARIES; SEMANTICS;

COMPLEX QUERIES; DECISION SUPPORTS; HETEROGENEOUS DATA SOURCES; QUERY EVALUATION; SCIENTIFIC DATA; SCIENTIFIC DISCOVERY; SEAMLESS INTEGRATION; SEMANTIC KNOWLEDGE;

DATA INTEGRATION;

EID: 84960917672     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2001.974408     Document Type: Conference Paper

References (68)

1. S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman. Basic Local Alignment Search Tool. Journal of Molecular Biology, 215(3):403-10, October 1990.
2. A. Bairoch and R. Apweiler. The SWISS-PROT protein sequence databank and its supplement TrEMBL. Nucleic Acids Res, 1(27):49-54, January 1999. http://www.expasy.ch/sprot.
3. A. Baxevanis. The molecular biology database collection. Nucleic Acids Research, 28(1):1-7, 2000. http://nar.oupjournals.org/cgi/content/ full/27/1/1.
4. P. Baker, A. Brass, S. Bechhofer, C. Goble, N. Paton, and R. Stevens. TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. An Overview. In Sixth International Conference on Intelligent Systems for Molecular Biology (ISBM98), 1998.
5. P. Buneman, J. Crabtree, S. Davidson, V. Tannen, and L. Wong. BioKleisli. BioInformatics, 1998. http://www.cbil.upenn.edu/K2/.
6. C. Baru, et al. XML-Based Information Mediation with MIX. In Proc. ACM SIGMOD Symp. on the Management of Data, pages 597-599, Philadelphia, Pennsylvania, 1999. demonstration session.
7. L. Bright, J-R Gruser, L. Raschid, and M.E. Vidal. A wrapper generation toolkit to specify and construc wrappers for web accessible data sources (websources). Journal of Computer Systems Science & Engineering. 14(2), March 1999.
8. D. Benson, I. Karsch-Mizrachi, D. Lipman, J. Ostell, B. Rapp, and D. Wheeler. GenBank. Nucleic Acids Res, 1(28):15-8, January 2000.
9. T. Berners-Lee, D. Connoly, and R. Swick. Web Architecture: Describing and Exchanging Data. W3C Note, 1999.
10. T. Berners-Lee, J. Hendler, and O. Lassila. The semantic web. Scientific American, May 2001.
11. S. Cluet, C. Delobel, J. Siméon, and K. Smaga. Your mediators need data conversion. In Proccedings of the ACM SIGMOD Conference, pages 177-188, 1998.
12. D. Chamberlin, D. Florescu, J. Robie, J. Siméon, and M. Stefanescu. XQuery: A Query Languagefor XML. W3C, 2000. available at http://www.w3.org/TR/xmlquery.
13. D. Chamberlin. A Complete Guide to DB2 Universal Database. Morgan Kaufmann, San Francisco, CA, 1998.
14. W.F. Cody, et al, Querying multimedia data from multiple repositories by content: The garlic project. In IFIP 2.6 (VDB-3), Lausanne, Switzerland, March 1995. http://www.almaden.ibm.com/cs/garlic.
15. I.A. Chen, A.S. Kosky, V.M. Markowitz, and E. Szeto. Constructing and Maintaining Scientific Database Views. In Proceedings of the 9th Conference on Scientific and Statistical Database Management, August 1997.
16. I.A. Chen and V.M. Markowitz. An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools. Information Systems, 20(5):pp 393-418, 1995.
17. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature, 409:860-921, February 2001.
18. T. Critchlow. Report on xewa-00: The xml enabled wide-area searches for bioinformatics workshop. Technical report, IEEE Computer Society, 2000.
19. L. Croft, S. Schandorff, F. Clark, K. Burrage, P. Arctander, and J. Mattick. Isis: The intron information system reveals the high frequencyof alternative splicing in the human genome. Nature Genetics, 24:340-341, 2000.
20. S. Davidson, J. Cabtree, B. Brunk, J.Schug, V. Tannen, C. Overton, and C. Stoeckert. K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal, 40(2):512-531, 2001.
21. S. Davidson, C. Overton, V. Tannen, and L. Wong. BioKleisli: A Digital Library for Biomedical Researchers. Journal of Digital Libraries, 1997.
22. T. Etzold and P. Argos. SRS, An Indexingand Retrieval Tool for Flat File Data Libraries. Computer Applications of Biosciences, 9(1):49-57, 1993. See also http://srs.ebi.ac.uk.
23. B. Eckman, A. Kosky, and L. Laroco. Extending traditional query-based integration approaches for functional characterization of post-genomic data. BioInformatics, 17(7):587-601, 2001.
24. D. Fensel, I. Horrocks, F. van Harmelem, S. Decker, M. Erdman, and M. Klein. OIL in a Nutshell. In Proceedings of the European Knowledge Acquisition Conference (EKAW'00). LNAI, Springer Verlag, 2000.
25. D. Florescu, A. Levy, and A. Mendelzon. Database techniques for the world-wide web: A survey. SIGMOD Record, September 1998.
26. D. Florescu, A. Levy, I. Manolescu, and D. Suciu. Query optimization in the presence of limited access patterns. In Proccedings of the ACM SIGMOD Conference, 1999.
27. L. Frank. Between genes and proteins: After dna, scientists face the complex world of rna. 2001.
28. E. Glemet and J-J. Codani. LASSAP: a LArge Scale Sequence compArison Package. Bioinformatics, 13(2):137-143, 1997.
29. GenBank. Growth of genbank. (available at http://www.ncbi.nlm.nih.gov/Genbank/).
30. GeneCards. http://bioinformatics.weizmann.ac.il/cards/. Weizmann Institute Genome Center and Bioinformatics Unit.
31. B. Graveley. Alternative splicing: Increasing diversity in the proteomic world. Trends in Genetics, 17(2):100-107, 2001.
32. J.R. Gruser, L. Raschid, V. Zadorozhny, and T. Zhan. Learning response time for websources using query feedback and application in query optimization. VLDB Journal, Special Issue on Databases and the Web, (1):18-37, 2000.
33. L. Haas, P. Kodali, J. Rice, P. Schwarz, and W. Swope. Integrating Life Sciences Data - With a Little Garlic. In IEEE BIBE Symposium. November 2000.
34. L. Haas, D. Kossmann, E. Wimmers, and J. Yang. Optimizing queries across diverse data sources. In Proceedings of VLDB Conference, 1997.
35. L. Haas, P. Schwarz, P. Kodali, E. Kotlar, J. Rice, and W. Swope. Discoverylink: A system for integrating life sciences data. IBM Systems Journal, 40(2), 2001.
36. Y. Ioanidis and Y. Kang. Randomized algorithms for optimizing large join queries. In Proccedings of the ACM Sigmod Conference, 1990.
37. G. Kemp, N. Angelopoulos, and P. Gray. A Schema-based Approach to Building a Bioinformatics Database Federation. In IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE), Published by IEEE Press, Washington, DC, November 2000.
38. G. Kemp, C. Robertson, and P. Gray. Efficient access to biological databases using CORBA. CCP11 Newsletter, 3.1(7), February 1999.
39. Z. Lacroix. Scientific Data Integration: Wrapping Textual Documents with a Database View Mechanism and an XML Engine. In IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE), Published by IEEE Press, Washington, DC, November 2000.
40. Z. Lacroix. Retrieving and Extracting Web Data with Search Views and an XML Engine. In International Workshop on Data Integration over the Web, Interlaken, Swizterland, June 2001.
41. A. Levy, A. Rajaraman, and J. Ordille. Querying heterogeneous information sources using source descriptions. In Proceedings of the VLDB Conference, 1996.
42. K. Morris. An algorithm for ordering subgoals in nail! In Proceedings of Symposium on Principles of Database Systems, 1988.
43. H. Naacke, G. Gardarin, and A. Tomasic. Leveraging mediator cost models with heterogeneous data sources. Proc. of ICDE, 1998.
44. Z. Nie and S. Kambhampati. Joint optimization of cost and coverage of information gathering plans. (submitted to publication), 2001.
45. PubMed. http://www.ncbi.nlm.nih.gov/pubmed/. National Library of Medecine.
46. Y. Papakonstantinou and V. Vassalos. Query Rewriting for Semistructured Data. In Proc. ACM SIGMOD Symp. on the Management of Data, pages 455-466, Philadelphia, Pennsylvania, 1999.
47. M. Rebhan, V. Chalifa-Caspi, J. Prilusky, and D. Lancet. GeneCards: A novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics, July 1998. available at http://bioinformatics.weizmann.ac.il/cards/CABIOS-paper.html.
48. M. Tork Roth, F. Ozcan, and L.Haas. Cost models do matter: Providing cost information for diverse data sources in a federated system. Proc. of VLDB, 1999.
49. M.T. Roth and P. Schwarz. Don't scrap it, wrap it! a wrapper architecture for legacy data sources. Proceedings of the International Conference on Very Large DataBases, 1997.
50. A. Sahuguet and F. Azavant. Building light-weight wrappers for legacy web data-sources using w4f. In Proceedings of the VLDB Conference, 1999.
51. P. Selinger, M. Astrahan, D. Chamberlin, R. Lorie, and T. Price. Access path selection in a relational database management system. In Proceedings of the ACM Sigmod Conf. on the Management of Data, 1979.
52. M. Steinbrunn, G. Moerkotte, and A. Kemper. Heuristic and randomized optimization for the join ordering problem. VLDB Journal, 6:91-208, 1997.
53. th International Conference on Intelligent Systems for Molecular Biology (ISBM), pages 272-281, Heidelberg, Germany, 1999.
54. A. Tomasic, L. Raschid, and P. Valduriez. Scaling access to distributed heterogeneous data sources with disco. IEEE Transactions On Knowledge and Data Engineering, 1998.
55. T. Urhan, M. Franklin, and L. Amsaleg. Cost-based query scrambling for initial delays. In Proccedings of the ACM SIGMOD Conference, 1998.
56. J. Ullman. Principles of Database and Knowledge-Base Systems, volume II. Computer Science Press, 1989.
57. J. Ullman. Information integration using logical views. In Proceedings of the Sixth International Conference on Database Theory, 1997.
58. UniGene. http://www.ncbi.nlm.nih.gov/unigene/. National Library of Medecine.
59. C. Venter et al. The sequence of the human genome. Science, 291:1304-1351, February 2001.
60. M.E. Vidal. Mediation Techniquesfor Multiple Autonomous Distributed Information Sources. PhD thesis, Universidad Simón Bolívar, Caracas, Venezuela, 2000.
61. V. Vassalos and Y. Papakonstantinou. Describing and using query capabilities of heterogeneoussources. In Proceedings of the VLDB Conference, 1997.
62. M.E. Vidal, L. Raschid, and J-R. Gruser. A meta-wrapper for scaling up to multiple autonomous distributed information sources. In In the Proceedings of the Intl. Conf. on Cooperative Information Systems, 1998.
63. G. Wiederhold. Mediators in the architecture of future information systems. IEEE Computer, pages 38-49, March 1992.
64. J.A. White et al. Guidelines for human gene nomenclature. Genomics, 45(2):468-471, 1997. See also http://ash.gene.ucl.ac.uk/nomenclature/.
65. L. Wong. Some MEDLINE Queries Powered By Kleisli. In ACCESS, June 1998.
66. L. Wong. Kleisli, its Exchange Format, Supporting Tools, and an Application Protein Interaction Extraction. In IEEE BIBE Symposium. November 2000.
67. R. Yerneni, C. Li, H. Garcia-Molina, and J. Ullman. Computing capabilities of mediators. In Proceedings of the ACM SIGMOD Conference, 1999.
68. V. Zadorozhny, L. Raschid, T. Zhan, and L. Bright. Validating a cost model for wide area applications. In Proceedings of the Intl. Conf. on Cooperative Information Systems, 2001.