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Partnership Identifies Chemical-Gene-Disease Interactions for Inclusion in Database

Carolyn Mattingly, Ph.D.
North Carolina State University
NIEHS Grants R01ES014065, R01ES019604

Environmental health researchers and pharmaceutical drug developers share the common goal of improving the ability to predict chemical toxicity. With this goal in mind, Pfizer safety scientists and the biocuration staff at the Comparative Toxicogenomics Database (CTD)  collaborated in text mining and manually reviewing more than 88,000 scientific articles to develop a dataset of adverse events from drugs. Funded in part by the NIEHS, this partnership demonstrates the benefits of resource sharing and collaboration between public and private entities with complementary needs.

CTD is a public database that promotes understanding about how the molecular interactions between environmental chemicals and genes affect human health. CTD curators use text mining and manual curation to convert knowledge from scientific papers into data on chemical-gene, chemical-diseases, and gene-disease interactions that can be more easily managed, queried, explored, and analyzed. The collaborating researchers text mined and manually reviewed 88,629 articles with information on the potential involvement of 1,200 pharmaceutical drugs in cardiovascular, neurological, renal, and hepatic toxicity. In one year, this process produced 254,173 toxicogenomic interactions, including 152,173 chemical-disease, 58,572 chemical-gene, and 5,345 gene-disease and 38,083 phenotype interactions. All of these interactions are fully integrated into the public CTD.

Citation: Davis AP, Wiegers TC, Roberts PM, King BL, Lay JM, Lennon-Hopkins K, Sciaky D, Johnson R, Keating H, Greene N, Hernandez R, McConnell KJ, Enayetallah AE, Mattingly CJ. 2013. A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions. Database (Oxford) 2013:bat080.


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