Joseph Leone[1], Dong-Guk Shin[2]
Interoperability with public genome databases is expected to be crucial m making the Human Genome Project a success. We propose to develop software tools in which users of the genome community can learn and/or examine public genome database schemas in a relatively short time and can produce a correct SQL expression easily. Specifically we aim at developing tools in which users access both GDB and GSDB simultaneously.
Initially we will focus on addressing one of the known key problems for making a distributed SQL interface practically useful. That is, a user who is not familiar with one of the two public genome databases would have difficulty understanding the schema of that database. Consequently, he may not be able to import relevant database schemas among many available ones and may have difficulty forming correct SQL expressions. In a federated database environment, this problem of dealing with unfamiliar third party database schemas becomes much more severe due to the manifold added complexity. Our proposed approach is to design features that aid users in understanding GDB and GSDB schemas quickly and embed them as a part of the proposed distributed SQL interface.
Another aspect of our effort focuses on testing the feasibility of using Galaxy graphical user interface development tool kit to build the proposed interface. Our ultimate goal is to make the interface system portable across multiple hardware platforms, i.e., Unix workstations, PCS and Macs. The proposed interface will be a client program, and by developing the client program to be portable across different platforms, the interface will be usable by the widest possible user groups.
[1] A. J. Boggs & Company, 2853 W. Jolly Road, Okemos, Michigan 48864. Work supported by a grant from the U.S. Department of Energy, under Contract No. DE-FG02-95ER81906.
[2] Computer Science & Engineering, University of Connecticut, Storrs, CT 06269-3155. Work done in collaboration with Genome Data Base, Johns Hopkins University, and supported by National Center for Human Genome Research, National Institute of Health, HG00772-01.