NIH awards grant to Stanford to launch Biomedical Computation Center

Stanford 29 September 2005The National Institutes of Health (NIH) have awarded the Stanford University School of Medicine a grant of $18,8 million to develop a National Center for Biomedical Ontology along with several other collaborating institutions. The goal of the centre is to design and implement a new generation of computer systems that will enable researchers to share, compare and analyse data gathered from large biomedical experiments. The centre will be led by Mark Musen, MD, PhD, professor of medicine (medical informatics), whose Stanford research group created Protege, the most widely used ontology-development software in the world.

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"It felt like a call from Ed McMahon", stated Mark Musen, who was at a conference in Madrid in July when an NIH official initially contacted him about his application. C. John Whitmarsh, PhD, acting director of the Center for Bioinformatics and Computational Biology, had called Mark Musen to inform him that Stanford was a serious contender for one of this year's three grants to develop a national biomedical computing centre. "I was surprised we were as well-received as we were", stated Mark Musen. "We're probably a bit more cutting-edge than is typical."

For decades, scientists have developed computational tools to analyse data collected in laboratories and clinics with the aim of answering specific biological questions. Because many of these databases have been designed independent from each other, they often are not compatible, making it difficult, if not impossible, to reach conclusions. But recent advances in technology, in particular the growing popularity in the use of ontologies, could make it possible to integrate the data from divergent studies.

And that's where Dr. Musen's centre comes into play. "Simply put, ontologies are ways of structuring knowledge so that computers can use it", Dr. Musen explained. "Ontologies define in computer-understandable form the concepts, and the relationships among concepts, that are important in particular application areas. Ontologies have become critical for processing and integrating disparate data sources. The data integration provided by ontologies enables computers to draw inferences from diverse medical experiments, providing the kind of understanding that ultimately can help combat diseases."

Key to getting the grant funded was Dr. Musen's proposal to draw support from colleagues across North America and the United Kingdom, each with their own expertise. Dr. Musen's application included the informatics group at the Berkeley Drosophila Genome Project, with its sustained support of the Gene Ontology Consortium and the Open Biomedical Ontologies library, as well as the Mayo Clinic, which is working to advance standards for the representation of clinical terminologies. Also involved are researchers from the University of Victoria in British Columbia and State University of New York-Buffalo.

In addition, three institutions will lead projects to apply the research and study the use of ontology services when addressing specific biomedical problems. Scientists at Cambridge University will explore how to use studies of mutations in fruit flies as models for understanding human diseases; researchers at the University of Oregon will explore the opportunities for analysing relationships between gene function in zebrafish and humans, and researchers at the University of California San Francisco (UCSF) Medical Center will explore how to combine the results from multiple randomized trials in the area of HIV/AIDS.

The project with UCSF is a good example of how the centre will try to make sense of difficult-to-reconcile results from randomized trials. According to Ida Sim, MD, PhD, associate professor of general internal medicine and associate director for medical informatics in the graduate programme in biological informatics at UCSF, there have been multiple trials on reducing mother-to-child transmission of HIV and the benefits of treatment interruptions for AIDS patients on anti-retroviral drugs.

But researchers have been unable to combine the results statistically and make comparisons because of their independent and different designs, she said. Dr. Sim will use the information-management tools of the centre to visualize, analyse and understand the valuable information from these trials to help advance HIV/AIDS care. It is hoped that research at the new centre also will lead to new ontological software tools to resolve similar dilemmas in the future. George Rutherford, MD, director of the UCSF Institute for Global Health, is also collaborating with Dr. Sim on the project.

Dr. Musen and the NIH are now accepting applications from researchers at campuses across the country who wish to work with the centre. If the agency accepts their proposals, these scientists can draw from NIH funding set aside specifically for this purpose. The NIH hopes to select more collaborative projects by the start of next year.

Stanford University Medical Center integrates research, medical education and patient care at its three institutions: Stanford University School of Medicine, Stanford Hospital & Clinics and Lucile Packard Children's Hospital at Stanford. For more information about the project you can visit the National Center for Biomedical Ontology Web site.


Leslie Versweyveld

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