Database Commons

a catalog of worldwide biological databases

Xanthusbase (http://www.xanthusbase.org), a model organism database for the bacterium Myxococcus xanthus, functions as a collaborative information repository based on Wikipedia principles. It was created more than 5 years ago to serve as a cost-effective reference database for M. xanthus researchers, an education tool for undergraduate students to learn about genome annotation, and a means for the community of researchers to collaboratively improve their organism's annotation. We have achieved several goals and are seeking creative solutions to ongoing challenges. Along the way we have made several important improvements to Xanthusbase related to stability, security and usability. Most importantly, we have designed and implemented an installer that enables other microbial model organism communities to use it as a MOD. This version, called Openmods, has already been used to create Xenorhabdusbase (http://xenorhabdusbase.bact.wisc.edu), Caulobacterbase (http://caulobacterbase.bsd.uchicago.edu) and soon Bdellovibriobase.

xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.