Appel: PSB 2012, Text and Knowledge Mining for Pharmacogenomics

Thierry Hamon thierry.hamon at UNIV-PARIS13.FR
Wed May 11 06:06:07 UTC 2011

Date: Sun, 8 May 2011 00:34:01 +0200
From: "Kevin B. Cohen" <kevin.cohen at>
Message-Id: <201105080034.02007.pz at>

CALL FOR PAPERS: Pacific Symposium on Biocomputing 2012

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

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


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

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