BUFFALO, N.Y. -- To tackle an increasing global infectious
disease burden and rising rates of drug-resistant infections,
University at Buffalo philosophers are working with medical
researchers to develop the first-ever infectious disease
Ontology is the science of how things are classified and the
relationships between them. When researchers in biology and
medicine use ontology classifications, they are able to speak the
By allowing geneticists, scientists and clinicians to easily
share and compare many different types of data about pathogens,
patients and disease processes, the ontology being developed by UB
philosophers and their colleagues will expedite the development of
new methods of diagnosis and treatment.
"Currently, the infectious disease data being collected by
hospitals and research centers lack a common framework to enable
integration and comparison of results," explained Barry Smith,
Ph.D., SUNY Distinguished Professor, Julian Park Professor of
Philosophy at UB and a pioneer of biomedical ontology. "The
Infectious Disease Ontology, which is being developed by ontology
experts at UB and startup firms in Buffalo, together with
immunologists and infectious disease researchers throughout the
world, will provide that common framework."
According to Smith, the need for an infectious disease ontology
has become more imperative as the incidence of infectious diseases
has increased, treatment has become more difficult and researchers
have responded by generating more data in the search for better
ways to diagnose and treat them.
Now, with a $1.25 million research grant from the National
Institute of Allergies and Infectious Diseases and $70,000 in pilot
funding from the Burroughs-Wellcome Fund, UB's Smith and Lindsay
Cowell of the Duke University Medical Center have initiated the
Infectious Disease Ontology, (IDO). They will test the IDO using
data from Staphylococcus aureus, (S.a.), one of the most
common and potentially deadly human infections in the U.S. and
Such interest has spurred not just the development of UB as an
international center of ontology, it also is beginning to attract
to Buffalo information technology firms eager to collaborate in
this vibrant and emerging field. Most recently, a satellite office
of Blue Highway, a wholly owned subsidiary of medical device
manufacturer Welch Allyn, has moved into UB's New York State Center
of Excellence in Bioinformatics and Life Sciences, to develop with
UB researchers new software and hardware technologies that take
advantage of biomedical ontology.
Also located in UB's Center of Excellence on the Buffalo Niagara
Medical Campus is the Ontology Research Group, which Smith
co-directs with Werner Ceusters, M.D., UB professor of psychiatry,
and Louis J. Goldberg, D.D.S., Ph.D., UB dean emeritus of the
School of Dental Medicine.
For the past four years, Smith has been working with the
developers of bio-ontologies, including the Gene Ontology, to
demonstrate how the lessons learned in philosophy and logic -- for
example, the proper use of definitions and classifications -- can
lead to improvements, which in turn can bring real benefits to
biological and clinical research.
"The use of ontologies by clinical researchers reflects
recognition of the need for common frameworks for integrating data
across biological and clinical disciplines," said Smith. "It also
reflects increasing efforts by the National Institutes of Health
and other bodies to encourage clinical researchers to make their
data more easily available to wider groups of researchers.
"The new approach to ontology, which we pioneered at UB, makes
it easier to build good quality ontologies in a consistent fashion
and to reason with the associated data in a way that is designed to
be easily extendible to new diseases and new pathogens," he
Other diseases being studied under the IDO Consortium
established by Smith and Cowell include malaria and other
vector-borne diseases, tuberculosis, infective endocarditis,
influenza and dengue fever.
Information on the initiative is available at http://infectiousdiseaseontology.org.
The four-year grant from NIAID, in which UB works as a
subcontractor to the Duke University Medical School with $250,000
in funding, will support the creation, application and testing of
an S.a. ontology as part of IDO.
"Our goal is to create the ontology and to apply it to predict
disease genes, testing our predictions against the large collection
of patient data that is being collected by the Duke
Staphylococcus aureus Bacteremia Group, led by Vance Fowler,
with whom we will collaborate in drawing consequences for
developing new sorts of patient-centered diagnosis and treatment,"
At the same time, the UB ontologists are strengthening their
relationships with companies like Blue Highway and others located
in or working with the Center of Excellence.
"Blue Highway researchers are addressing the problems that arise
when integrating heterogeneous sorts of data -- in this case, the
real-time data collected through the use of new medical
technologies to support early detection, diagnosis and aggregation
of data for comprehensive clinical support," said Smith. "The
collaboration between Blue Highway and UB's Ontology Research Group
will allow rapid and focused testing of ontological ideas in
contexts of real-world, practical applications. We believe that
this will bring improvements to both sides, both in ontologies and
in the technologies that use them to collect and reason with
Albert Goldfain, Ph.D., a Blue Highway researcher and recent UB
graduate who works in in the UB Center of Excellence, noted that
Infectious Disease Ontology research will be among the first
efforts to integrate ontology data across many different scales, an
important and difficult issue for biomedical applications.
"While some research has been done on individual genes, for
example, and other ontology work has been done on whole organisms,
these data have all been developed in separate information silos,"
he said. "The Infectious Disease Ontology will cross-cut ontologies
developed by others at different scales; it will draw and map
relationships at the level of individual molecules, cells, organs,
organisms and populations, and ultimately a way to speed diagnosis
In addition to their research on IDO, researchers from UB and
Blue Highway will collaborate on other areas of joint research:
these include technologies with potential applications in alarm
management and data aggregation. Additional areas of potential
collaboration include communications protocols for military
applications, power management, materials science and battery
technology, as well as biosensors and lab-on-a-chip
"Blue Highway has a working relationship with UB and is
exploring technologies of interest in the area of health care,"
said Jack Rudnick, senior vice president of legal and government
affairs at Blue Highway. "Blue Highway is occupying space in UB's
downtown Center of Excellence to facilitate the relevant research
and leverage the excellent working opportunities with students,
researchers and staff. We look forward to realizing some of the
exciting opportunities that collaboration with UB provides."
The University at Buffalo is a premier research-intensive public
university, a flagship institution in the State University of New
York system and its largest and most comprehensive campus. UB's
more than 28,000 students pursue their academic interests through
more than 300 undergraduate, graduate and professional degree
programs. Founded in 1846, the University at Buffalo is a member of
the Association of American Universities.