| Joint effort to make biological databases compatible |
EMBRACE: European Model for Bioinformatics Research and Community Education
EMBRACE is younger than BioSapiens, but it too is concerned with the need for a unified bioinformatics approach in Europe. Whereas BioSapiens’ focus is on data analysis, the goal of EMBRACE is to improve access to biological information for scientists both inside and beyond European borders.
Launched in February 2005, it brings together computational biologists from 17 institutes in 11 countries to tackle the problem of the incompatibility of existing biological databases. “The complication is that the connections between the different biological information resources do not reflect the ‘joined-up’-ness of the science behind them,” says EMBRACE coordinator Graham Cameron of the European Bioinformatics Institute in Hinxton, UK.
Finding a solution
At the moment, a researcher interested in the genetic basis of disease, for instance, might have to search ten or more databases to find all the existing information relating to a particular set of candidate genes he or she is interested in. Data providers work very hard to produce databases that are comprehensive, user-friendly and cross-linked to other databases, but different providers use different methods.
The solution is probably not a monolithic system for storage of all biological information, says Cameron, because such systems have been proved inadequate in the past. Rather, EMBRACE aims to offer researchers simultaneous access to many different information resources.
The project partners will exploit state-of-the-art computational and e-science methods to devise database interfaces that conform to certain standards, so that out of the numerous existing databases will emerge an overarching data grid – the EMBRACEgrid – through which users can access information dispersed through the various resources, as seamlessly as possible.
Cameron says that EMBRACE is a timely response to various pressures coming to bear on biological researchers. From a scientific perspective, the emphasis is now on systems rather than components. In the post-genomic era, researchers are moving away from the study of sequences and chunks of genetic information to that of pathways and interactions. “A purely component-based approach wouldn’t allow you to get to grips with that,” he explains.
And the fragmentary nature of the current system for organising information shows up most clearly when new resources come on-line. “Until relatively recently, if you had some new resource – be it a tool or database – that wanted to expose itself to the biological community and become linked into it, there were very few protocols for doing that,” says Cameron. “Now, however, there is a consensus emerging.”
As part of the network’s activities, a “technology watch” will be mounted to make sure that the grid does not get locked into technology that is likely to become outdated quickly. The grid will also be regularly challenged by test problems, like that of identifying candidate disease genes, to ensure that it is functioning as well as it can.
Educating scientists about the EMBRACEgrid will be key to the project’s success, not only by ensuring that they use it, but also so that they begin to “grid-enable” their own databases, thereby expanding the EMBRACEgrid.
The European Bioinformatics Institute
The European Molecular Biology Laboratory
The Wellcome Trust Genome Campus, HINXTON
CB10 1SD Cambridge, Great Britain
Tel: + 441223494467
Fax: + 441223494486
EC Funding: €8.280.000
Duration: 5 years