[Elsnet-list] CFP: PSB 2012, Text and Knowledge Mining for Pharmacogenomics

Pierre Zweigenbaum pz at limsi.fr
Sun May 8 00:34:26 CEST 2011

From: "Kevin B. Cohen" <kevin.cohen at gmail.com>

CALL FOR PAPERS: Pacific Symposium on Biocomputing 2012

Text and Knowledge Mining for Pharmacogenomics: Genotype-phenotype-drug


The technical area of this session is text and knowledge mining for
pharmacogenomics, particularly focusing on genotype-phenotype-drug
relationships.  Broad categories of work that have been well-studied in the
past are included, specifically text mining and reasoning, but submissions
are restricted to applications of that work to the constrained area of
pharmacogenomics, and particularly genotype-phenotype-drug relationships.
For example, topics that are solicited include:

- Relation extraction between genotypes, phenotypes, and drugs, and other
semantic classes relevant to pharmacogenomics
- Corpus development for pharmacogenomics text mining
- Work on the corpus of documents linked to by PharmGKB
- Reasoning systems applied over the PharmGKB knowledge base

Work on gene taggers would not be considered for inclusion.  However, work
on named entity taggers for other relevant semantic classes, such as drugs
and phenotypes, would be considered responsive to the call for papers.

This is a full session, not a workshop, and all accepted papers will be
published in the PSB proceedings and indexed in PubMed/MEDLINE.  PSB has
long been considered a high-prestige conference for publication of BioNLP
papers, and some of the papers from PSB NLP sessions have gone on to be
quite influential, such as Fukuda et  al. (1998) on gene mentions and
Schwartz and Hearst (2003) on abbreviation definitions.


- Paper submissions due: July 18, 2011, midnight Pacific (note that this is
a one-week extension past the normal PSB deadline)
- Notification of paper acceptance: September 9, 2011
- Final paper deadline: September 23, 2011, midnight PT
- Meeting: January 3-7, 2012


Please see http://compbio.ucdenver.edu/PSB2012/submission.shtml.


Kevin Bretonnel Cohen, U. Colorado School of Medicine
Yael Garten, Stanford University
Nigam Shah, Stanford University
Udo Hahn, Universität Jena

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