Bioinformatics adventures in database research.pdf

Bioinformatics Adventures in Database Research Jinyan Li, See-Kiong Ng, and Limsoon Wong Laboratories for Information Technology 21 Heng Mui Keng Terrace, Singapore 119613 Email: jinyan, skng, limsoon
@lit.a-star.edu.sg Abstract. Informatics has helped launch molecular biology into the genomic era. It appears certain that informatics will remain a major contributor to molecu- lar biology in the post-genome era. We discuss here data integration and datamin- ing in bioinformatics, as well as the role that database theory played in these top- ics. We also describe LIMS as a third key topic in bioinformatics where advances in database system and theory can be very relevant. 1 The Great Challenges in Bioinformatics Bioinformatics is key to genome projects. The main challenges are to improve the con- tent and utility of databases, to develop better tools for data generation, capture, and an- notation, to develop and improve tools and databases for functional studies, to develop and improve tools for representing and analysing sequence similarity and variation, and to create mechanisms to support effective approaches for producing robust software that can be widely shared. In the 1990s, a lot of databases were produced by the numerous mapping and sequencing initiatives. The hot topics were problems of managing and integrating these databases, and of comparing and assembling sequences contained in these databases. In the 2000s, several genomes have been completely sequenced and we enter the era of post-genome knowledge discovery. The hot topics are problems of rec- ognizing specific features and functions of DNA and protein sequences, understanding their role in diseases, and their interaction with each other and their environment. We focus on two stories. The first story concerns data integration challenges in bioinformatics in the 1990s. We narrate the triumph of the theory of query languages and the Kleisli system [6, 39, 9] in addressing these challenges. The second