The Kleisli Query System

Participants: Peter Buneman, Jing Chen, Susan Davidson, Kyle Hart, Thangavelu Kandasamy, Kui Lin, Hai Liu, Daphna Strauss, Val Tannen, Jiren Wang, Limsoon Wong, Oliver Wu

Background

Achievements

• The first general broad-scale integration system that solved a number of the so-called ``impossible'' bioinformatics data integration problems described in the 2003 DOE Bioinformatics Summit Report.

• Transparently extended almost all standard RDBMS into nested relational DBMS, supporting a nested relational version of SQL with the ability to query across heterogeneous data sources that are geographically dispersed.

• Commercialized in 1998 by GeneticXchange Inc., and deployed in a number of large pharmaceutical companies (e.g., Schering Plough, SmithKlineBeecham). Following acquisition by GE Healthcare, the system is marketed under the name ``Discovery Hub''.

• Considered one of the six major practical achievements in functional programming by experts of the field. [P. Wadler, ``An angry half dozen'', ACM SIGPLAN Notices, 33(2):25-30, 1998.]

• Won multiple awards. In particular,
  • The 1997 Tan Kah Kee Young Inventors Gold Award. This is one of the only two gold award in the open category ever given in the 20-year history of the Tan Kah Kee Young Inventors Award Competitions
  • The 1998 ASEAN Certificate of Achievements
  • The 1999 Singapore Youth Award

Selected Publications

• Peter Buneman, Susan Davidson, Kyle Hart, Chris Overton, Limsoon Wong. A Data Transformation System for Biological Data Sources. Proceedings of 21st International Conference on Very Large Data Bases, Zurich, Switzerland, 158-169, September 1995. PS

• Wang Chiew Tan, Ke Wang, Limsoon Wong. QUICK: Graphical User Interface to Multiple Databases. Proceedings of 7th International Workshop on Database and Expert Systems Applications, Zurich, Switzerland, 404-409, September 1996.

• Susan Davidson, Chris Overton, Val Tannen, Limsoon Wong. BioKleisli: A Digital Library for Biomedical Researchers, International Journal of Digital Libraries, 1(1):36--53, April 1997. PS

• WangChiew Tan, Ke Wang, Limsoon Wong. A Graphical Interface to Genome Multidatabases, Journal of Database Management, 9(1):24--32, Winter 1998.

• O. P. Wu, K. T. Seow, L. Wong, S. Y. Chung, S. Subbiah. From Sequence to Structure to Literature: The Protocol Approach to Bioinformation. Proceedings of Pacific Symposium on Biocomputing'98, Maui, Hawaii, pages 747--758, January 1998. (Invited paper.)

• Jing Chen, Limsoon Wong, Louxin Zhang. A Protein Patent Query System Powered By Kleisli. Proceedings of ACM SIGMOD International Conference on Management of Data, Seattle, Washington, pages 593--595, June 1998. PS

• Jing Chen, Nam-Hai Chua, Daphna Strauss, Limsoon Wong. Extracting Kozak Consensus Sequence Using Kleisli. Proceedings of 1st International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, August 1998, pages 218--223. PS

• Thangavelu Kandasamy, HweeHwa Pang, Allison Ting, Jiren Wang, Limsoon Wong. Two Tools for Solving Bioinformatics Problems. Proceedings of 1998 IEEE Knowledge and Data Engineering Exchange Workshop, Taiwan, November 1998, pages 79--86.

• Kui Lin, Anthony E. Ting, Jiren Wang, Limsoon Wong. Hunting TPR Domains Using Kleisli, Proceedings of 9th Workshop on Genome Informatics, Tokyo, Japan, December 1998, pages 173--182. PS

• Jing Chen, Daphna Strauss, Limsoon Wong. Using Kleisli to bring out features in BLASTP results. Proceedings of 9th Workshop on Genome Informatics, Tokyo, Japan, December 1998, pages 102--111. PS

• Susan Davidson, Peter Buneman, Jonathan Crabtree, Val Tannen, Chris Overton, Limsoon Wong. BioKleisli: Integrating Biomedical Data and Analysis Packages. Bioinformatics: Databases and Systems, chapter 17, pages 201--212. Kluwer Academic, Boston, 1999.

• Su-Yun Chung, Limsoon Wong. Kleisli, a new tool for data integration in biology. Trends in Biotechnology, 17(9):351--355, September 1999. PDF

• Jiren Wang, Limsoon Wong. An Example in Kleisli: Codon Usage Extraction Made Easy. Science Asia, 25:23--29, 1999. (Reviewed invited paper.) PS

• Limsoon Wong. Kleisli, a Functional Query System Journal of Functional Programming, 10(1):19--56, January 2000. (Reviewed invited paper.) PDF

• Limsoon Wong. The Functional Guts of the Kleisli Query System. ACM SIGPLAN Notices, 35(9):1--10, 2000.

• Limsoon Wong. Kleisli, its Exchange Format, Supporting Tools, and an Application in Protein Interaction Extraction, Proceedings of IEEE International Symposium on Bio-Informatics and Biomedical Engineering, Washington DC, November 2000, pages 21--28. PS, PPT

• Limsoon Wong. Bioinformatics Takes Charge. Proceedings of 10th International Conference on Biomedical Engineering, Singapore, December 2000, 45--46. (Invited paper.) PS, PPT

• Limsoon Wong. Visualization and Manipulation of Pedigree Diagrams. Proceedings of 11th Workshop on Genome Informatics, Tokyo, Japan, December 2000, pages 63--72. Talk. PS, PPT

• Jing Chen, Limsoon Wong. Turning Relational DBMS into Nested Relational DBMS. Unpublished manuscript, March 2001. PS.

• Limsoon Wong. Bioinformatics Integration Simplified: The Kleisli Way. Frontiers in Human Genetics: Diseases and Technologies, chapter 6, pages 79--90. World Scientific, Singapore, 2001.

• Limsoon Wong. Technologies for Integrating Biological Data. Briefings in Bioinformatics, 3(4):389--404, 2002. (Reviewed invited paper) PDF

• Jing Chen, Su-Yun Chung, Limsoon Wong. The Kleisli Query System as a Backbone for Bioinformatics Data Integration and Analysis. Bioinformatics: Managing ScientificData, chapter 6, pages 147--187, Morgan Kaufmann, San Francisco, CA, 2003. PS

• Susan Davidson, Limsoon Wong. The Kleisli Approach to Data Transformation and Integration. The Functional Approach to Data Management: Modeling, Analyzing, and Integrating Heterogeneous Data, chapter 6, pages 135--165. Springer-Verlag, September 2003. PS

• Limsoon Wong. Technologies for Biological Data Integration. The Practical Bioinformatician, chapter 17, pages 375--400, World Scientific, May 2004. PS

Selected Presentations

• Kyle Hart, Limsoon Wong, Chris Overton, Peter Buneman. Querying Heterogeneous Biological Data Sources. Talk given at Meeting on Genome Mapping and Sequencing, Coldspring Harbor, New York, May 1994.

• Limsoon Wong. Industry Perspective and Software Development: Hunting for Domains in Style. Invited talk at Consultative Roundtable Workshop on the Implementation of National Bioinformatics and Biotechnology Network (NABBINet), Bangi, Malaysia, August 1998.

• Limsoon Wong. Extracting Features from BLASTP Results. Invited talk at BioMedInfo Singapore'98, Singapore, September 1998.

• Limsoon Wong. Bioinformatics Integration Simplified: The Kleisli Way. Invited talk at International Symposium on Human Genetics and Gene Therapy, Singapore, February 1999. PS

• Limsoon Wong. The Functional Guts of the Kleisli Query System. Invited keynote at 5th ACM SIGPLAN International Conference on Functional Programming, Montreal, Canada, September 2000.

• Limsoon Wong. The Functional Guts of Kleisli. Invited talk at KAIST Advanced Information Technology Research Center, Taejon, Korea, November 2000. PPT

• Limsoon Wong. Databases and information Discovery. Invited talk at Post-Genome Knowledge Discovery Program Master Class on Language of DNA, Institute for Mathematical Sciences, Singapore, February 2002.

Acknowledgements