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Dutch bioinformatics community highly visible in IMI

NBIC

23 Sep 2010

The Open Pharmacological Space (OPS) project and the Drug Disease Modelling Resources (DDMoRe) consortium have been selected for funding by the European Innovative Medicine Initiative (IMI). NBIC researchers play a central role in these two large-scale projects, which focus on interoperability and modelling respectively.

Unique assertions
"The amount of information that is available in the life sciences field is overwhelming, but it is stored in numerous different databases that all employ different terminology", says Barend Mons (NBIC/LUMC), who is an initiator of the Open Pharmacological Space (OPS) project (total budget: €20 million) and a member its steering committee. "Also the data itself differs greatly, there is genomics data, transcriptomics, proteomics, etc. Our main challenge is interoperability, making sure that these different databases can 'talk' to each other. To this end, we will translate all the 'assertions' in the life science into unique concept triples, which we call 'nanopublications'. All the information amounts to roughly 10^14 triples right now, but we can bring that down to 200 billion unique assertions. That number makes it feasible to start in silico knowledge discovery."

Global standard
Next to the LUMC and NBIC, also Maastricht University and the University of Amsterdam are partners in the OPS project, creating a highly visible role for the Dutch bioinformatics community. That visibility is further enhanced by the involvement of the Leiden Institute of Advanced Computer Science (LIACS) and the Leiden Amsterdam Centre for Drug Research (LACDR) as key partners in the Drug Disease Modelling Resources (DDMoRe) consortium, which also boasts a total budget of €20 million. "Modelling plays a central role in clarifying the mode of action of a drug and models are an essential part of the filing dossier of newly developed drugs. With DDMoRe, we aim to set a global standard for the description of such models", Joost Kok (NBIC/LIACS/LUMC) explains. "Here in Leiden, we will primarily focus on designing a Model Description Language and the tools associated with such a design. This will involve the application of the technology behind programming languages. From an informatics point of view, it will be very interesting to apply text and data mining technology developed within NBIC to this type of biological models." Barend Mons agrees: "In fact, the evaluators of both projects and also the one selected for Electronic Medical Records, strongly advocated that the three projects operate on the ‘same ontological framework’ making modelling, in silico discovery and translation to patients one interoperable space."

Adoption by users

DDMoRe is in essence an infrastructure project and the success will ultimately be measured by the adoption of the Drug Disease Model Library Framework by pharmaceutical companies. "Translating our work to the end users is crucial", says Joost Kok. "After all, our ambition is to create a global standard in this field. It is good to mention here that valuable work on drug/disease modelling already has been done by the Top Institute Pharma in the Netherlands, which we can use as a basis for this project." There is a clear link with the OPS project, although both endeavours have completely different starting points. Joost Kok: "We start from the mathematical modelling side, more top down, whereas the OPS project is really data driven. But in the end, we will meet and it will be interesting to connect our models to the systems biology field."

Innovative Medicine Initiative
The Innovative Medicine Initiative (IMI) is a partnership between the European Commission and the European Federation of Pharmaceutical Industries and Associations (EFPIA). Main objective of the IMI is to support the overall drug discovery and development process by tackling pre-competitive bottlenecks in R&D that are too large and too complex for individual parties to take on. The European Commission has dedicated €1 billion to IMI, which will be matched by the pharmaceutical industry, bringing the total budget to €2 billion for the period 2007-2013.

More on IMI: www.imi-europe.org

Interview on Open Pharmacological Space: http://www.youtube.com/watch?v=qB1ljMvGxXg