The Pharmacogenomics Knowledge Base (PharmGKB) is an integrated resource about how variation in human genetics leads to variation in response to drugs.

As part of our work in the SASEBio project, we have processed a version of PharmGKB (Sep. 30th, 2010) with our OG-RM (OntoGene Relation Miner) tool. We have downloaded all PubMed abstracts which have annotated relations in PharmGKB. Using only entities provided by PharmGKB, we have automatically annotated the abstracts, see example below (genes in blue, drugs in green, diseases in yellow):

We have automatically generated candidate relationships by combining the terms extracted in each abstract - using a number of different techniques, each of which we have evaluated against the "gold standard", which in this case is the manually annotated relationships provided by PharmGKB.

The set of annotated abstracts is made accessible through our ODIN advanced interface: ODIN-pharmgkb (WARNING: tested only on Firefox and Safari!!!!)

Instructions on how to use the demo can be found here.

The results of this activity have been initially presented at the workshop  "Mining the Pharmacogenomics Literature" of the Pacific Symposium on Biocomputing (PSB 2011).

Fabio Rinaldi, Gerold Schneider, Simon Clematide. Mining complex Drug/Gene/Disease relations in PubMed. Proceedings of the workshop "Mining the Pharmacogenomics Literature", Pacific Symposium on Biocomputing, Hawaii, January 2011.

The results of a collaborative experiment on interactive curation, in collaboration with the PharmGKB group, have been presented at the International Conference on Biocuration 2012, and are described in the following journal paper.

Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl-Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, and Russ B. Altman. Using ODIN for a PharmGKB revalidation experiment. The Journal of Biological Databases and Curation, Oxford Journals, 2012, bas021; doi:10.1093/database/bas021

If you find this work interesting please cite the paper above, and, as a reference to PharmGKB, the following:

T.E. Klein, J.T. Chang, M.K. Cho, K.L. Easton, R. Fergerson, M. Hewett, Z. Lin, Y. Liu, S. Liu, D.E. Oliver, D.L. Rubin, F. Shafa, J.M. Stuart and R.B. Altman, Integrating Genotype and Phenotype Information: An Overview of the PharmGKB Project, The Pharmacogenomics Journal (2001) 1, 167-170.

Below some additional screenshots.