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ProteoMonitor BIND Gets Paid, But Will Its Database Become the Standard?

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By Julia Karow

 

After two years of waiting for its first big paycheck, the Biomolecular Interaction Network Database is finally bringing home the bacon. Having secured funding from its new industry partner Sun Microsystems, BIND can now access almost $14 million in Canadian government funds, and is set to act on its stated goal of becoming “the world’s most comprehensive repository for biomolecular interaction data.” However, what remains to be seen is whether proteomics researchers will accept BIND as the standard for protein interaction data.

In mid-June, the Blueprint Initiative, the administrator for BIND, finally secured C$29 million in funding, which includes previously announced awards of C$12.5 million from Genome Canada and C$5.4 million from the Ontario Government’s Research and Development Challenge Fund, as well as C$1 million from the Canadian Institutes of Health Research.

Although the players behind BIND first announced their plans for the database in June of 2001, their funding has only become available now due to some twists and turns in industry support for the project. Changing the Canadian government’s pledges to contribute into signed checks required BIND to find industry partners willing to participate in funding the project. Now, with an additional C$10.1 million, largely from Sun Microsystems, as well as MDS Proteomics and Foundry Networks, BIND can get busy. “An in-kind match from Sun and other industrial partners was absolutely required to get the cash flow from our government agencies,” Chris Hogue, who runs Blueprint as the principal investigator at the Samuel Lunenfeld Research Institute in Toronto, wrote in an e-mail.

The process took two years because IBM, one of BIND’s original partners, backed out. IBM and MDS Proteomics each pledged C$4.5 million in cash and equipment back in June of 2001, but “IBM could not come to terms with its promised contribution,” Hogue says, and MDS Proteomics — itself not loaded with cash — contributed equipment worth C$2 million only “up to November 2002.”

With funding secured, Blueprint plans to rapidly expand BIND. At the moment, it has a staff of 59, including 12 database curators, 29 software developers, students, administrative, and other staff, but it plans to expand to 77 by 2005. Over the last year, database entries have already more than doubled, from about 7,000 interaction, pathway, and molecular complex records to about 18,000, most of these from yeast. By mid-2005, Blueprint wants to get up to 50,000 records, as well as release new software and related tools such as visualization modules.

Some scientists, though, are reluctant to commit to one database just yet. A team led by Marc Vidal, an assistant professor at Harvard Medical School who studies protein networks in C. elegans and yeast, uses a number of interaction databases for its research. These include not only BIND, but also the Database of Interacting Proteins, which is maintained at the University of California, Los Angeles and contains 18,494 interactions to date, as well as the MIPS yeast protein interaction database, maintained in Munich. Moreover, Vidal’s group finds it easier to download large datasets directly from researchers’ websites, rather than from a database. With regard to DIP and BIND, Vidal says, it’s “still a bit too early” to say which one is better.

While acknowledging the desirability of a central repository that will archive interaction data permanently and serve as a hub for data submissions, Vidal says he is not sure whether any of the existing databases is up to the task yet. For now, he prefers that interaction databases stay compatible with each other, for example by participating in HUPO’s Proteomics Standards Initiative, which has been working on an XML model for the exchange of protein interaction data. “In this field, I am not sure yet that anybody can impose their standard,” Vidal says.

 

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