SGER: A Collaborative Information Repository Model Organism Database

模式生物数据库(MODS)已成为生命科学研究不可或缺的工具。MODS使合作教育项目成为可能，提供了一个中央信息交换中心来共享资源、传播信息，也许最重要的是，通过汇编、吸收和组织不同的数据源来催化新的发现。典型的MOD是一个基于互联网的注释，构建在基因组序列的“脚手架”上。所有其他数据--如微阵列结果、突变菌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联系。但大多数MOD都在努力解决所有动态数据库都面临的问题：确保所有数据都是完整、最新和准确的。现有的维护和更新内容的方法成本很高，而且不能可靠地请求、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。本项目的目标是进一步开发黄色粘球菌的模式生物数据库。XanthusBase项目(http://www.xanthusBase.org))将在企业界和公共互联网数据库中吸取的经验教训纳入到设计和实施一种新的模式，该MOD采用了维基百科(http://www.wikipedia.org))的编辑原则，作为一个自愿合作的信息储存库。维基编辑原则规定：1)所有用户都可以立即访问编辑；2)所有编辑都被永久保存；3)任何编辑都可以很容易地恢复到以前的状态。这种方法是基于这样一个假设，即研究人员是MOD的主要用户，是该模式生物(MO)的最重要的专家，通过确保数据的完整、最新和准确，他们可以获得最大的收益。因此，维基编辑提供了以最低的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，并适用于其他模式生物。

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.