Tuesday, April 24, 2012

Text-Mining tool revalidated by the PharmGKB Curators

Keeping up with the ever-growing large volume of scientific articles published each day is a challenge, and there is a need for efficient text-mining tools that could support curation of this information.

The PharmGKB Scientific Curators worked with informaticians at the Institute of Computational Linguistics in Switzerland to test and develop a text-mining tool called ODIN (OntoGene Document INspector) that identifies articles with drug-gene relationships. The tool highlights the genes and drugs within the article abstract and enables the user to view the results, and check or modify the entities that have been annotated automatically by the system.

The results of the revalidation study are published in Database:

"Using ODIN for a PharmGKB revalidation experiment"
Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl-Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, Russ B. Altman. Database, Vol 2012, Article IA bas021, doi: 10.1093/database/bas021
Read the PDF