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UW-Madison joins effort to build public pathogen bioinformatics database

Scanning electron micrograph of E. coli. Source: NAIAD Biodefense.
MADISON - In an effort to speed up research on disease-causing pathogens, including ones that could be used as biological weapons, scientists at the University of Wisconsin-Madison will team with an information technology company, SRA International, Inc., to build an online, publicly accessible library of data on these infectious agents and their genomes.

The work is part of an estimated $13.6 million, five-year contract awarded to SRA by the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, and will represent one of multiple newly established Bioinformatics Resource Centers for Biodefense and Emerging/Re-emerging Infectious Diseases, each focusing on a different set of animal and human pathogens.

The resource, called ERIC (Enteropathogen Resource Integration Center), is already onlne. As more information is collected and analyzed, the site will be updated.

Designed to facilitate scientific research, the resource will consolidate known information about enterobacteria, a group of pathogens that can cause diseases such as dysentery, plague and typhoid fever. The site will also include information on diarrheagenic E. coli, one of the most-studied species in modern biology.

In addition to providing a picture of these genomes - all of the genes in an organism - the resource will bring together information about what these genes do and which ones are shared across organisms. Any publications identifying the genes or their roles also will be listed. Plus, researchers using the database can make direct contributions, adding new pieces of information to complete the picture.
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"Currently, this information is really disparate," said Nicole Perna, an assistant professor of animal health and biomedical sciences at the UW-Madison School of Veterinary Medicine, who will lead the university's involvement in this collaborative project. "This resource will be a one-stop shop that will facilitate a lot of different research projects and cut down on the time researchers need to spend correlating information from separate resources."

Many of the genomes that will be included on this Web site were sequenced on campus, and some of the technology the resource will utilize was developed here. For example, an analysis tool created by a UW-Madison graduate student to identify genes common across organisms will be integrated into the Internet resource.

"The researchers at the University of Wisconsin-Madison are among the world's experts on the genomes of these enteropathogens," said Timothy Cooke, SRA's vice president and director of health systems. "We look forward to this collaboration, combining SRA's experience in bioinformatics IT development with UW-Madison's domain expertise."

Perna said, "We will be users as well as developers of the technology and information."

Besides being a boon to the research community and the the public, who ultimately will benefit from the progress made on the study of these pathogens and the diseases they cause, Perna says the resource may aid researchers, such as herself, who study closely related organisms that are not considered potential bioterrorism agents.

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