GIS, bioinformatics collaborations offer promising new perspectives

June 28, 2001

BLACKSBURG, Va., June 28, 2001 - The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoæand its roster of renowned participants from both fieldsæhas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area.

GIS and bioinformatics have much in common, most notably digital maps, large databases, and research involving visualization, pattern recognition, and analysis. In general, researchers use GIS techniques and tools to find and track large patterns, for example, geographic distribution of cancer and other diseases in human, animal, and plant populations. Researchers in bioinformatics generally look at very small patterns, such as those in DNA structure that might predispose an organism to developing cancer.

Geoff Jacquez, chairman and chief scientist of TerraSeer, which distributes environmental and health sciences software, said, "The joining of genomics and proteomics with GIS and spatial epidemiology has the potential to provide an enormous breakthrough.

"In the past, GIS and spatial epidemiology focused on finding and monitoring large-scale, population-based occurrences such as disease clusters, outbreaks of infection, or possible associations between cancers and environmental factors," Jacquez continued. "But this exercise was mostly limited to generating hypotheses, not facts.

As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous."

James B. Campbell, head of Virginia Tech's geography department and an organizer of the conference, said exchanges across the disciplines are mutually beneficial. "Whether the maps used in a discipline are derived from aerial photos taken by a satellite, as with GIS, or discoveries at the microscopic level that are mapped by gene researchers, many of the processes and technologies are similar or the same," he said.

Virginia Bioinformatics Institute (VBI) Director Bruno Sobral agreed. "The notion of a map goes all the way from the level of a genome to a map of the United States," he said. "Bioinformatics has focused on modeling from the level of the molecules up to the whole organism, while GIS has created tools to model from the level of the ecosystem down." Sobral said this makes the individual organism "a perfect meeting point for the two communities."

Jacquez described what was, from his perspective, the symposium's biggest take-home lesson: "After years of using GIS data to track diseases in populations in terms of the what, where, and when, the integration of bioinformatics data--genomics and proteomics data telling the story of what takes place at the cell and sub-cell level in individual diseased organisms--will soon enable epidemiologists using GIS to capture the how of disease outbreaks." Integrating bioinformatics with GIS, he said, will be "phenomenally useful" in predicting public health outcomes.

Encouraging dialog among the fields, Sobral said, will enable researchers using GIS, for instance epidemiologists, to home in on individual cases. At the same time, he said, geneticists will be able to widen their purview, "noting, for example, how the incidence of congenital disease varies over space, over time, and with changes to terrain and climate."

Broad interplay between geography and biology isn't entirely new. Software companies such as GIS giant ESRI and Jacquez's TerraSeer have for some time marketed software for health and natural resources applications. Representatives of both companies were in attendance, however, to survey some of academe's first steps into a new area. They also shared perspectives from the marketplace on GIS's future in bioinformatics and on applications of GIS to environmental epidemiology and ecology.

Shared technical challenges and applications relevant to both disciplines were other topics for discussion. Both fields rely heavily on mining, managing, accessing, and analyzing large amounts of data, and the disciplines share many of the same challenges for data management and representation, said Carol Bult of the University of Maine, who created the first direct application of GIS technology to bioinformatics and hosted the first spatial genomics workshop in 1997.

"We learned that many solutions to technical problems arrived at in one discipline can serve as object lessons for the other." Bult added that when some of the display and interactivity features of GIS maps are ported to genomics maps, genetic maps will go from being mere display tools to serving as interactive "mechanisms for discovery."

Campbell said other possible long-term outcomes of connecting the two investigative fields are better modeling of the spread of insect infestations, for instance that of the gypsy moth in the United States; better monitoring of diseases such as rabies in wildlife populations; improvements in agricultural productivity; and reductions in the negative environmental impacts of some agricultural activities. "The cross-pollination of research accomplished by the symposium," he said, "will accelerate multiple outcomes not even yet envisioned."

The seeds of collaboration have long been embedded in the lexicon and metaphors of both fields. Genomics participants' language was ripe with references to genetics stated in geospatial termsæ"deserts" of uncharted genetic space, "neighborhoods" of genes, and genetic "pathways," for example. When a GIS researcher borrowed one of Sobral's slides defining bioinformatics and noted that most of the text still applied when "GIS" was exchanged for "bioinformatics," it was clear that the fields define their needs in silkjkljmilar ways.

According to GIS expert Michael Goodchild of UC-Santa Barbara, the meeting was long needed. "In GIS and bioinformatics there is increasing need to share data among researchers, policy makers, and the general public," he said. Goodchild noted that, more than ever before, the Internet, the World Wide Web, and digital library technology are helping to make data-sharing possible. "This new collaboration between GIS and bioinformatics will allow us to exchange experiences, methods, and best practices in data sharing."
-end-
Also featured was the work of Barbara Buttenfield, of the University of Colorado, Stephanie Green of Washington State, John Havlin of North Carolina State, and Bill Carstensen (geography) and Randy Wynne (forestry), directors of Virginia Tech's Office of GIS and Remote Sensing, one of the conference sponsors, along with VBI and the provost's office at Virginia Tech.

Proceedings, which consist of streaming video files and associated slide presentations, are available at http://www.vbs.vt.edu/A1GISBIO/GISBIO.html.

Contacts for additional information: Bill Carstensen, carstens@vt.edu, 540-231-2600, http://gis.lib.vt.edu/VT_OGIS. Bruno Sobral, bioinfo@vt.edu 540-231-2100, http://www.vbi.vt.edu.

PR CONTACT: Jeanne M. Garon, 540-231-7188, jgaron@vt.edu.

Faculty contact: James B. Campbell Jr., 540-231-5841, jayhawk@vt.edu.

Virginia Tech

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