A major hurdle faced by molecular biologists doing large scale DNA sequencing and gene mapping involves the efficient handling and analysis of the voluminous data that is acquired. The goal of this project is to prototype an object-oriented database for genome analysis and to demonstrate the effectiveness of the resulting prototype system. We initially used the mapping and sequencing data of the model organism E. coli , but the system will be extended to include human genome data. E. coli genome data and programs are provided by Kenneth Rudd of NCBI. Human genome data are provided by Robert Robbins of GDB. Previously using Rudd's E. coli genome data and analysis programs we have demonstrated that they can be successfully integrated into a commercial object-oriented database system. This proposal focuses on the next phase of the work: to exploit the advantages offered by such an integration. The resulting object-oriented database system is expected to demonstrate significant advantages over its counterpart relational database system. It incorporates sophisticated integrity checking features, user-friendly graphical interfaces, efficient batch processing mechanisms, history tracking features, and typical user query handling mechanisms. We plan to make direct comparisons between our prototype system and its relational counterparts. We plan to use the end product for other related exploratory work such as interconnecting with established relational databases for cross-referencing. Our system will be deployed for actual laboratory evaluation by biologists.
