Funding Cuts Threaten Big Data

Reduced support from the US National Library of Medicine threatens to shut down five popular biological databases.

By | September 5, 2012

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In 2007, the US National Library of Medicine (NLM) shunted millions of dollars away from infrastructure grants, which supported widely used databases that house terabytes of biological data, and instead invest those resources in informatics research, Nature reported. As a result, at least five such databases are now facing serious funding shortages and are on the brink of being shuttered.

“The idea that this resource could just disappear is a serious problem for everyone who relies on it,” Mark Musen, a bioinformatician at Stanford University in California, and manager of one such database called Protégé, told Nature.

“As journals, we cannot host all the data that are part of the paper, and so if they disappear, it’s a big deal,” Inês Chen, chief editor at Nature Structural and Molecular Biology (NSMB) said in the same article.

But the databases are not going down without a fight from their user communities. This week more than 90 scientists wrote letters to NSMB in support of the Biological Magnetic Resonance Data Bank (BMRB), which contains thousands of entries on the nuclear magnetic resonance of biomolecules used by structural biologists around the world. The BMRB has been funded by the NLM since 1990, but is now looking to other federal funders, according to University of Wisconsin-Madison’s John Markley.

Protégé, which has 200,000 registered users, is also looking for federal funding, specifically from the National Institutes of Health (NIH), as Musen feels strongly that charging scientists for access would discourage them from using the site at all. Last June, Musen submitted an NIH grant application, but it was rejected, despite having been accompanied by more than 100 letters of support. Musen is still awaiting a decision on his resubmitted application.

Another option is commercial sponsors. New England Biolabs, for example, already partially support a database of enzyme data called REBASE, and will take on the full costs of the database when its federal support runs out in 2014, CSO Richard Roberts, who also founded of REBASE, told Nature.

Unfortunately, the drought in federal funding is unlikely to change any time soon. “The whole system is rigged against infrastructure of any kind,” Princeton genomicist David Botstein, a member of the NIH working group that drafted a report on the issue in June, told Nature.

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