Wednesday, August 15, 2012

Mining the pharmacogenomics literature

Briefings in Bioinformatics Special Issue: Current Progress in Bioinformatics 2012 contains an editorial by Russ Altman discussing the current status of bioinformatics research.

Among the articles in this special issue is a review on the current status of techniques for mining of the pharmacogenomics literature and includes descriptions of studies that have utilized the corpus of human-curated pharmacogenetic (PGx) articles in PharmGKB to train or assess the accuracy of machine-learning methods.

"The PharmGKB repository comes perhaps closest to the vision of an all-embracing pharmacogenomics corpus. It represents a major step towards an interdisciplinary biomedical information store." quote from: 

Mining the pharmacogenomics literature -- a survey of the state of the art. Hahn U, Cohen KB, Garten Y, Shah NH. Brief Bioinform. 2012 Jul;13(4):460-94.

At the PharmGKB we are currently working on a natural language processing (NLP) pipeline that would assist in the identification of relevant PGx articles for our curators to then manually curate.