For the Sake of Research and Patient Care, Scientists Must Find Common Language

Biomedical ontology conference shows how philosophers are helping this massive endeavor

Release Date: June 27, 2011 This content is archived.


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Barry Smith is among prominent researchers who will gather in Buffalo next month in an effort to develop a common vocabulary for medicine and health care.

BUFFALO, N.Y. -- In July, hundreds of international scientists from dozens of biomedical fields will meet at the University at Buffalo seeking a common language with which to energize cross-disciplinary research.

The International Conference on Biomedical Ontology will take place July 26-30, and conference convener Barry Smith, PhD, says attendees have a common goal: to enable all of the data produced by the entire spectrum of life sciences to be easily retrieved and understood by those working in all biomedical fields, from the molecular to the global scale.

"It is a huge order," he says, "little understood by the general public and difficult to achieve, but absolutely necessary for the continued development of biomedical science. It promises benefits in some ways similar to those brought to physics by the standardization of units of measure in the 18th century."

The goal is so important, that Smith, an internationally-recognized medical ontologist, Julian Park Chair and SUNY Distinguished Professor of Philosophy at UB, has devoted his professional life to this endeavor.

The public may assume that when biomedical scientists talk, they use the same words to mean the same things. But as Smith points out, in different research fields, even such common terms as "pain," "gene," "blood" and "cancer" may have very different meanings as used in different contexts. With the exponential growth of biomedical data, this simple fact has enormous implications. It leads to incompatibilities that frequently confuse, halt cross-disciplinary research and severely limit communication among researchers.

"In order to advance science," he says, "it is crucial to successful biomedical research that researchers in various disciplines, from molecular biology to public health, who write in different languages and use discrete reporting schemes, accurately translate terms used by all systems in which they operate.

"Otherwise, meaning is lost. Information pertaining to research results cannot be found, in ways which can have devastating consequences to medical research," Smith says.

"Shared ontologies, which are agreed-upon systems of meaning are designed to prevent this from happening, to enhance knowledge among systems that could not otherwise talk to each other," he says.

"We not only need to develop and populate ontologies," Smith says, "but encode shared definitions in a way that enables computer programs to use them, and then promulgate our results to researchers throughout the world so that they understand this new knowledge and have functional access to it."

To these ends, this conference is one of a series initiated in 2009 to offer a forum for representatives of all major communities involved in the development and application of biomedical and related ontologies.

In addition to many scientific presentations, the conference will offer poster sessions, tutorials, workshops, and demonstrations of new software critical to translational research.

Among the issues under discussion this year will be techniques and technologies for collaborative ontology development, reasoning with biomedical ontologies, the evaluation of biomedical ontologies and how biomedical ontologies interact with the Semantic Web (i.e., the "web of data" that enables machines to understand the semantics, or meaning, of information on the World Wide Web).

Smith says presenters will consider these issues in connection with gene and cell research, biomedical imaging, biochemistry and drug discovery, biomedical investigations, experimentation, clinical trials, clinical and translational research, and development and anatomy

Keynote speakers will be Bernard de Bono, MD, PhD, of the European Bioinformatics Institute, and Roberto Rocha, MD, PhD, senior corporate manager for knowledge management and clinical decision support in the Clinical Informatics Research and Development (CIRD) group of Partners Healthcare and Harvard School of Medicine.

De Bono's talk on the "Virtual Physiological Human Project," will address efforts to bring together physiology and pharmacology modelers to develop uniform representation for anatomical structure and function by increasing the interoperability of clinical systems.

Rocha's talk, "Practical Applications of Ontologies in Clinical Systems," will address his work with Partners Healthcare and at the University of Utah (2000-08), where he led the design and implementation of a distributed data and knowledge management infrastructure to support clinical and translational research.

UB presenters include Werner Ceusters, MD, professor of psychiatry, UB School of Medicine and Biomedical Sciences, and principal investigator on a new National Institutes of Health grant focused on an ontology for pain and related disability, mental health and quality of life. He will present a tutorial at the conference to illustrate how this developing ontology can help patients with chronic pain clearly and accurately express how they feel to the doctors and healthcare providers trying to understand and treat them.

Other UB presenters include, in addition to Smith, Alex Diehl of the Department of Neurology, Randall Dipert of the Department of Philosophy, Patrice Seyed of Computer Science, and Alan Ruttenberg of the School of Dental Medicine.

Further information, including the program and a list of the 150 participants registered thus far, can be found at

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