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PSI Knowledgebase Set to Roll in 2007

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Since its launch in 2000, the Protein Structure Initiative of the National Institutes of General Medical Science has progressed at a good clip. The initiative has already completed a pilot phase to determine the structure of more than 1,000 proteins, set up new centers to triple that amount in the next five years, and launched a repository to store and distribute expression clones. One resource that's had to wait, however, is the Structural Genomics Knowledgebase, a central hub to capture the project's data. The wait may soon be over.

The request for applications to host and coordinate the Knowledgebase was initially issued in December 2005, but the award of $2.5 million was not made on schedule last fall. According to Jerry Li, program director at the NIGMS Center for Bioinformatics and Computational Biology, the problem was that none of the applicants had sufficient expertise to pull off the job alone.

As Genome Technology's sister publication Bioinform reported last November, NIGMS did consider re-announcing the RFA, in addition to other options. According to that announcement, the Knowledgebase is described as a Web portal and data repository for all resources produced by the PSI. Knowledgebase functions specifically include managing targets selected by PSI centers, developing a system of structural and functional annotation, and supporting the computational modeling of protein structures. "I think the reason no one did really well in the review process was because we were asking for something that really hasn't been done before," Li says.

However, Li notes that re-announcing the RFA would essentially require another year of review and deployment -- all while PSI centers would be cranking out new data that would be difficult to capture in retrospect.

NIGMS and PSI center leaders met in early December to come up with an alternative plan. As the centers themselves already have bioinformatics components in place to capture specific data types, Li says, "and because the mission of the Knowledgebase is so intimately bundled with the mission of the centers," PSI center leaders agreed to come together as a consortium to perform the functions of the database. "Everyone agrees that the Knowledgebase should be established as soon as possible, without delay," Li says, "so the proposal made by the centers is a sensible solution."

Essential activities of the Knowledgebase will now be enacted by PSI centers, while other activities will be subcontracted to outside groups on a project basis. The only thing left is to identify a project leader to coordinate all of these activities, Li says.

NIGMS plans to hire a part-time senior researcher or investigator to oversee the budget, personnel, and coordination of the Knowledgebase. "Basically, the institute will hire an independent chief operating officer to lead the structural dynamics projects," Li says. This project leader will report to the institute, but will also have guidance from a so-called board of directors partly composed of the program director of the PSI, steering committee chairs, and some of the center directors, Li says.

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