By John Russell
Feb. 14, 2008 | After just a few months of close collaboration with the Cystic Fibrosis Foundation Therapeutics (CFFT), GeneGo has launched MetaMiner CF, a disease-specific tool embedded in GeneGo's MetaCore pathway database and analysis platform. The new tool contains rich information about cystic fibrosis and represents an important expansion by GeneGo into disease-specific areas.
"CFFT approached GeneGo because we were looking for an informatics tool that would help integrate emerging data from biomarker and target identification projects with the known literature," says Diana Wetmore, VP of alliance management for CFFT (a non-profit drug discovery and development affiliate of the Cystic Fibrosis Foundation).
"What evolved was a collaborative effort. We recruited top CF academic and clinical researchers to work with the GeneGo developers. The researchers helped the developers and annotators comb through the literature to filter out dated and misleading information and focus on the literature known to be most relevant today," she says.
The new tool, launched last week, is available at a discount to the roughly 4000 members of the Cystic Fibrosis Foundation. It's available at normal pricing to all researchers as part of the GeneGo's MetaCore platform according to Julie Bryant, GeneGo VP of business development.
Because CF experts were involved, "[T]he information is current and based upon the latest understanding of disease mechanism. For instance, there has been a shift in the understanding of how TLR4 receptors in lung epithelium are involved generating an inflammatory response to bacteria," says Jerry M. Wright, a project collaborator and researcher at Johns Hopkins Medical Institutions Department of Physiology. "Five or ten years from now it would be generally accepted but would be difficult to pick out by a non-expert from current literature. This knowledge is reflected in the GeneGo map connections and the information on record justifying why this connection exists and why it disagrees with previously published studies."
Making things even more difficult, says Wright, is that CF is a disease that progresses over decades, affects multiple organ systems in a variable manner, and end-stage bacterial infection no longer has direct connection to the original gene defect. Presenting that in a 2-dimensional map environment is challenging. "An additional issue of great importance is that the maps and networks will be periodically evaluated by CF experts and updated if necessary," he says.
Wetmore suggests CF researchers might tackle several challenges with MetaMiner CF, including using the signaling networks to correlate proteomics data that might point to new therapeutic targets; using the CFFT canonical maps to get quickly to the key literature; identifying new patterns of linked effects from complex micro-array data; and creating visual displays of complex information that can be used as communication and collaboration tools.
Within the Cystic Fibrosis Foundation, she says, "MetaMiner CF will have a dramatic impact on our ability to visualize complex information and help us prioritize research initiatives."
CF researcher Raymond Frizzell of the University of Pittsburgh School of Medicine was a key collaborator and agrees the tools will help fill needed gaps.
"It is impossible to keep all of the literature in one's head," says Frizzell, "but more importantly, the maps will help us be open to other possible interpretations for the data that we collect, by informing us that we are perturbing an entire system when we are testing a very specific hypothesis. Second, we will be able to approach the maps quantitatively and therefore rank the significance of various pathways in affecting the CF related outcomes we study."
"Third, the CF field is always leading us into parts of the biological petri dish that we didn't anticipate, and the maps and the extended MetaCore structure will reduce or flatten the learning curve for moving into new areas. Fourth, it will permit young investigators who are entering the field to access and understand it more quickly, and for someone like me, the daunting area of infection/immunity can be better understood and perhaps even approached experimentally."
At the beginning of the CFFT collaboration last summer, Bryant noted it would be "the first in the series of disease-centered MetaMiner projects." That the project was able to be completed so quickly bodes well for future disease-centered efforts.