A Pilot Database for Collaborative Studies of Human Genome Diversity

这是一项由将参与人类基因组多样性计划（HGDP）试点项目的许多不同国家的一组研究人员探索使用公共数据库的建议。更大的HGDP项目仍处于规划阶段，但信息学显然将发挥关键作用；鉴于此，HGDP的组织结构包括一个信息学委员会（由冷泉港的Tom Marr博士担任主席）。该委员会建议，原型开发是项目早期阶段信息学的一个重要方面。在耶鲁，我们开发了一个客户端-服务器数据库来处理我们自己的数据，这些数据非常类似于将在试点项目和完整的HGDP中收集的数据。因此，HGDP信息学委员会建议我们考虑调整我们的数据库作为试点项目使用的原型。这项提议是为了让基金进行这种转换。现有的数据库使用Macintosh上的4th Dimension作为客户端，Sun Sparcstation-2上的Sybase作为服务器；交流是通过互联网进行的。拟议的适应过程将涉及就初步修改进行广泛协商，随后将原型分发给几个不同国家的群体，进行第二轮修改，并由参与HGDP试点项目的至少10个实验室分发和使用。加州和康涅狄格州、日本、英国、德国和意大利的实验室已经被确定为参与者。这些实验室将在本地机器上使用耶鲁大学生产的客户端软件，将数据输入耶鲁大学的Sybase数据库。除其他方面外，将对数据库进行严格审查，以了解它如何能更好地促进数据的当地管理和数据收集过程，以及它如何能更好地促进项目的互动/协作性质。最终的数据集将向公众开放，并将作为进一步探索与更大HGDP相关的信息学的测试平台。本项目由体质人类学计划和生物科学数据库活动共同资助。

This is a proposal to explore use of a common database by a group of investigators in many different countries who will be participating in a Pilot Project of the Human Genome Diversity Project (HGDP). The larger HGDP Project is still in the planning stages but informatics will clearly play a crucial role; acknowledging that, the HGDP organizational structure includes an Informatics Committee (chaired by Dr. Tom Marr, Cold Spring Harbor). That Committee has recommended that prototype development is an important aspect of informatics at this early stage of the project. At Yale we have developed a client-server database to handle our own data which are very similar to the data that will be collected in the Pilot Project and in the full HGDP. Therefore, the Informatics Committee of the HGDP recommended that we consider adapting our database as a prototype for use in the Pilot Project. This proposal is for the funds to make that conversion. The existing database uses 4th Dimension on a Macintosh as the client and Sybase on a Sun Sparcstation-2 as the server; communication is over the Internet. The adaptation process proposed will involve wide consultation on an initial modification, distribution of the subsequent prototype to groups in several different countries, a second cycle of modification, and distribution and use by a minimum of ten laboratories participating in the HGDP Pilot Project. Laboratories in California and Connecticut, in Japan, in England, in Germany, and in Italy have already been identified as participants. Those labs will use the client software produced at Yale on their local machines to enter their data into the Sybase database resident at Yale. Among other aspects the database will be critically examined to see how it could better facilitate local management of data an the data collection process and how it might better promote the interactive/collaborative nature of the project. The final dataset will be publically available and will se rve as a testbed for further exploration of informatics relevant to the larger HGDP. This project is funded by both the Physical Anthropology Program and the Database Activity in the Biological Sciences.