Toronto bioinformatics program makes final pitch to keep research database in Canada

By Debbie Lawes

The principal researcher at Mount Sinai Hospital’s Blueprint Initiative hopes public money will be found soon to prevent a proteomics database – the largest of its kind in the world — from moving from Toronto to Singapore. Dr Christopher Hogue says the research program needs about $6.5 million annually to continue operations. His group is meeting with representatives from the federal granting councils, the Canada Foundation for Innovation (CFI) and federal and provincial governments in an eleventh hour attempt to stave off closure.

The non-profit Blueprint has already begun winding down operations. It laid off 33 people on May 2, about half of its staff, and has shifted some operations to its Blueprint Asia facility in Singapore.

“The government of Singapore is saying they have quite an appetite to pick up the research project because they see it as a great way to train their people and make them better scientists and to create commercial opportunities in Singapore,” says Eric Andrade, Blueprint’s managing director, global.

Blueprint’s 2002 funding from Genome Canada and other partners is set to expire June 30 (see box). Its recent application for $26 million over four years to develop new bioinformatics software tools was turned down by Genome Canada, largely because matching funding was not guaranteed.

“The project went through financial due diligence but didn’t pass the mustard largely on account that the province (Ontario) had not stated clearly that it was backing the project,” says Hogue, who was one of several researchers who returned or emigrated to Canada to work on Blueprint’s Biomolecular Interaction Network Database (BIND).

Unlike many other provinces, Ontario has a poor track record in providing matching funding for Genome Canada projects. In the 2002 competition, the Ontario R&D Challenge Fund contributed about $5.4 million, but that fund has since been consolidated into the new Ontario Research Fund (ORF), which isn’t yet accepting applications. Dr Tim McTiernan, ADM research and commercialization at the Ministry of Economic Development and Trade, says there will be a call for ORF proposals “in the next little while”.

While it’s too late for ORF to rescue Blueprint’s Genome Canada application, McTiernan says other options are being discussed. “Our officials along with several other funding agencies have been meeting to get more details of the nature of the project (Blueprint) and its ongoing needs in the context of our funding process.”

Genome Canada’s VP communications, Marcel Chartrand, says ongoing negotiations with the Ontario government have failed to resolve the matching funding problem. “Historically, (Ontario) has not supported Genome Canada projects, contrary to Quebec, BC, Alberta, and Saskatchewan,” says Chartrand. “Through the Ontario Genomics Institute, we are talking to Ontario to demonstrate how important genomics research is in the province and to seek their participation, but it hasn’t been easy in the last couple of years unfortunately. … We’re not losing hope, but it has been difficult.”

FUNDING OPTIONS

Hogue says Blueprint faces two funding hurdles: the need for interim cash to sustain it beyond June 30, and a federal-provincial deal that provides sustainable funding over the longer-term. “I think the short-term solution is going to have to come out of Ontario or some other province that is interested in the project. That will need to be followed by some sort of funders’ meeting with the federal granting councils, including CFI, to sort out if this is a priority for Canada.”

One idea Blueprint has pursued, unsuccessfully, is linking BIND with the National Research Council’s CISTI library. In the US, the National Centre for Biological Information is part of the National Institute of Health’s National Library of Medicine. “To our frustration, we’ve presented that story for the past two and a half years to the NRC … but to no avail, says Hogue.” Another option is a joint funding arrangement between Canada and Singapore, adds Andrade.

Established in 1999, BIND has evolved into the world’s largest free repository for proteomics data. The online resource contains more than 170,000 interactions, in addition to 9.3 million small molecule protein interactions. Blueprint has agreements with 77 scientific journals to tap into new peer-reviewed research, and several companies resell BIND data using customized software. US scientists are the largest users.

“We really are dominating in the biological data management space globally,” says Andrade. “I’m very hopeful that opinion leaders and government officials are now really turning their minds to this to think through a solution.”

Blueprint has also spun off two companies this year — Unleashed Informatics Ltd and Watershed Devices Ltd.

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