[BioNLP] New publications on text mining meets pharmacogenomics

Joerg Hakenberg joerg.hakenberg at gmail.com
Wed May 9 13:21:03 EDT 2012

Several articles on "Mining the Pharmacogenomics Literature" have just been
made available as online pre-prints with JBI.

They will be bundled into a special issue at some point---for now, you have
to look through
and find, for instance,

Using PharmGKB to Train text mining approaches for identifying potential
gene targets for pharmacogenomic
*In Press, Accepted Manuscript*, *Available online 4 May 2012*
S. Pakhomov, B.T. Mcinnes, J. Lamba, Y. Liu, G.B. Melton, Y. Ghodke, N.
Bhise, V. Lamba, A.K. Birnbaum

A knowledge-driven conditional approach to extract pharmacogenomics
specific drug–gene relationships from free
*In Press, Uncorrected Proof*, *Available online 27 April 2012*
Rong Xu, QuanQiu Wang

Development of a benchmark corpus to support the automatic extraction of
drug-related adverse effects from medical case
*In Press, Uncorrected Proof*, *Available online 25 April 2012*
Harsha Gurulingappa, Abdul Mateen Rajput, Angus Roberts, Juliane Fluck,
Martin Hofmann-Apitius, Luca Toldo

The EU-ADR corpus: Annotated drugs, diseases, targets, and their
*In Press, Uncorrected Proof*, *Available online 25 April 2012*
Erik M. van Mulligen, Annie Fourrier-Reglat, David Gurwitz, Mariam
Molokhia, Ainhoa Nieto, Gianluca Trifiro, Jan A. Kors, Laura I. Furlong

Systematic identification of pharmacogenomics information from clinical
trials <http://www.sciencedirect.com/science/article/pii/S1532046412000585>
*In Press, Uncorrected Proof*, *Available online 23 April 2012*
Jiao Li, Zhiyong Lu

A SNPshot of PubMed to associate genetic variants with drugs, diseases, and
adverse reactions<http://www.sciencedirect.com/science/article/pii/S1532046412000597>
*In Press, Uncorrected Proof*, *Available online 30 April 2012*
Jörg Hakenberg, Dmitry Voronov, Võ Hà Nguyên, Shanshan Liang, Saadat Anwar,
Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral

I apologize for most likely having missed a few---some text miner should
write a script to scan through that webpage and pick all TM/NLP-related
There are quite a few in press that are not related to the special issue as

Take care,
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