OBJECT-ORIENTED DABABASE FOR GENOME ANALYSIS

分子生物学家在进行大规模DNA研究时面临的一个主要障碍是 测序和基因定位涉及有效的处理和分析 大量的数据。该项目的目标是 为基因组分析建立面向对象的数据库原型， 验证了原型系统的有效性。我们 最初使用模式生物E的定位和测序数据。 大肠杆菌，但该系统将扩展到包括人类基因组数据。E. 大肠杆菌基因组数据和程序由NCBI的Kenneth Rudd提供。人类 基因组数据由GDB的RobertRobbins提供。 以前使用陆克文的E。大肠杆菌基因组数据和分析程序 证明了它们可以成功地整合到商业中， 面向对象的数据库系统这一建议侧重于下一阶段 这项工作的目的是：利用这种一体化所提供的优势。的 由此产生的面向对象的数据库系统，预计将展示 它比对应的关系数据库系统具有显著的优势。它 集成了先进的完整性检查功能， 图形界面，高效的批处理机制，历史 跟踪功能和典型的用户查询处理机制。我们计划 将我们的原型系统和它的关系 同行我们计划将最终产品用于其他相关的探索性研究。 工作，如与已建立的关系数据库互连， 交叉比对我们的系统将部署到实际的实验室 生物学家的评价。

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.