University at Buffalo - The State University of New York

Published: October 6, 2005

By PATRICIA DONOVAN
Contributing Editor

The University at Buffalo is one of eight institutions that will be affiliated with a new National Center for Biomedical Ontology established by the National Institutes of Health at the Stanford University School of Medicine.

Also collaborating with the center, established through a five-year, $18.8 million grant, are the Berkeley Drosophila Genome Project, the Mayo Clinic and the University of Victoria in British Columbia. Scientists at Cambridge University, University of Oregon and University of California-San Francisco Medical Center also will work with the new center.

The goal of the center is to design and implement a new generation of computer systems that will enable researchers to share, compare and analyze data gathered from large biomedical experiments.

Barry Smith, SUNY Distinguished Professor and Julian Park Chair in the Department of Philosophy, College of Arts and Sciences, will direct the Buffalo site of the center, leading its efforts to establish and disseminate good practices in ontology development, drawing on 30 years of experience as a philosopher working in the ontological domain.

Smith has an international reputation for his work in biomedical ontology and in 2001 received a $2 million Wolfgang Paul Award from Germany's Humboldt Foundation, believed to be the largest single prize ever awarded to a philosopher.

He said that scientists from the institutions affiliated with the new center and others institutions "will work toward designing and implementing a new generation of ontological theories and computer systems that will enable researchers to share, compare and analyze data gathered from large biomedical experiments."

The UB team also includes Werner Ceusters of the European Centre for Ontological Research, and Fabian Neuhaus, postdoctoral fellow in the Department of Philosophy.

"Through a number of recent hires, the UB Department of Philosophy has established itself as the pre-eminent center of theoretically grounded research in both formal and applied ontology," Smith said.

"The founding of the National Center of Biomedical Ontology, responding to the real needs of biologists and biomedical researchers," he said, "is a welcome confirmation of the importance of our work. It is also a valuable compliment to the resources of the New York State Center of Excellence in Bioinformatics and Life Sciences."

Smith is a member of the Center of Excellence's Data Intensive Analytical Bioinformatics Core Group. He and his work have received financial support from the Center of Excellence.

The new center is a response to urgent problem of communication across the disciplines related to the increasing use of computers in biomedical research.

Chemists, biologists, pharmacologists, epidemiologists and researchers in the many subfields of clinical medicine each have their own systems for classification and organization of their data that do not have the same meaning for those in other biomedical disciplines. The fact that so much data cannot be shared in a comprehensive, meaningful way seriously impedes biomedical research.

Ontology, a discipline that lies at the interface between philosophy and information science, is designed to solve such problems.

"Simply put, ontologies are ways of structuring knowledge so that computers can use it," said Mark Musen, director of the new center and a leading Stanford University ontologist and medical informatician.

"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," he added. "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."

In addition to the National Center for Biomedical Ontology, the NIH this year established the National Center for Integrative Biomedical Informatics at the University of Michigan and the National Center for Multi-Scale Study of Cellular Networks at Columbia University.

Along with four centers that the NIH created last year, the three new centers "will serve as the core of a universal computing infrastructure, allowing the biomedical community—including researchers and physicians—to seamlessly integrate, analyze, model and share data on human health and disease," according to the NIH.