SGER: A Collaborative Information Repository Model Organism Database

SGER：协作信息存储模型生物数据库

• 批准号: 0729638
• 负责人: Roy Welch
• 金额: --
• 依托单位: Syracuse University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2009-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0729638&HistoricalAwards=false
• 关键词: SGER; Collaborative; Information; Repository; Model

Model organism databases (MODs) have become an integral tool for life science research. MODs enable collaborative education projects, provide a central clearinghouse to share resources, disseminate information, and, perhaps most importantly, catalyze new discovery by compiling, assimilating and organizing disparate data sources. The typical MOD is an internet-based annotation constructed around the "scaffold" of a genome sequence. All other data -- such as microarray results, data for libraries of mutant strains, and journal articles -- are arranged within this structure and linked to locations on the genome sequence. But most MODs struggle with an issue faced by all dynamic databases: assuring that all data is complete, current, and accurate. Existing methods of maintaining and updating content are costly, and cannot reliably solicit, acquire, or even accommodate new data accruing at an ever-accelerating rate. Moreover the methods do not include a mechanism to assign meaningful credit to contributors. The goal of this project is to develop further the model organism data base for Myxococcus Xanthus. The xanthusBase project (http://www.xanthusBase.org) incorporates lessons learned in the business community and by public Internet databases into the design and implementation of a novel MOD for M. xanthus that employs editing principles from Wikipedia (http://www.wikipedia.org) to function as a voluntary collaborative information repository (CIR). Wiki-editing principles dictate that: 1) all users have immediate editorial access; 2) all edits are saved in perpetuity; and 3) any edit can be easily reverted to a previous state. This approach is based on the postulate that researchers, the primary users of a MOD, are the foremost experts for that model organism (MO), and have the most to gain by assuring that data is complete, current, and accurate. Thus Wiki-editing offers the best opportunity to optimize editorial accuracy at minimum maintenance cost. The scaffold will be fully transportable and applicable to other model organisms.

模式生物数据库（MOD）已成为生命科学研究不可或缺的工具。 MOD 支持协作教育项目，提供中央交换所来共享资源、传播信息，并且也许最重要的是，通过编译、同化和组织不同的数据源来促进新发现。典型的 MOD 是围绕基因组序列的“支架”构建的基于互联网的注释。所有其他数据——例如微阵列结果、突变株文库数据和期刊文章——都排列在这个结构中，并与基因组序列上的位置相关联。但大多数 MOD 都在努力解决所有动态数据库都面临的问题：确保所有数据完整、最新且准确。现有的维护和更新内容的方法成本高昂，并且无法可靠地征求、获取甚至容纳以不断加速的速度积累的新数据。此外，这些方法不包括向贡献者分配有意义的信用的机制。该项目的目标是进一步开发 Xanthus 粘球菌的模式生物数据库。 xanthusBase 项目 (http://www.xanthusBase.org) 将商业界和公共互联网数据库的经验教训纳入 M. xanthus 的新型 MOD 的设计和实施中，该 MOD 采用维基百科 (http://www.wikipedia.org) 的编辑原则来充当自愿协作信息存储库 (CIR)。维基百科的编辑原则规定：1）所有用户都可以立即进行编辑； 2）所有编辑永久保存； 3) 任何编辑都可以轻松恢复到之前的状态。这种方法基于这样的假设：研究人员（MOD 的主要用户）是该模式生物 (MO) 的最重要专家，并且通过确保数据完整、最新和准确而获得最大收益。因此，维基编辑提供了以最低维护成本优化编辑准确性的最佳机会。该支架将完全可运输并适用于其他模型生物。