SGER: A Collaborative Information Repository Model Organism Database

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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.