[Corpora-List] Call for Participation: PSB workshop on Mining the Pharmacogenomics Literature

[Kevin B. Cohen]

Call for Participation: Pacific Symposium on Biocomputing workshop on Mining
the Pharmacogenomics Literature

The aim of this workshop is to bring together researchers working on the
automatic extraction of relationships between biomedical entities from
research literature.  The workshop will focus particularly on methods for
the extraction of genotype-phenotype, genotype-drug, and phenotype-drug
relationships and their use for advancing pharmacogenomic research.  Efforts
aimed at creating benchmark corpora as well as comparative evaluation of
existing relationship extraction methods are of special interest.

Important dates

Abstract deadline: August 31, 2010
Speaker notification: September 15, 2010
Workshop: TBA, but some time January 3-7 2011, during PSB

Pharmacogenomics is both a timely and important field.  The promise that it
holds for individualized medicine may be on the crest of realization due to
technical advances like large SNP microarrays and analytical advances that
allow us to predict beneficial, non-beneficial, and deleterious drugs for
specific individuals based on aspects of both the individual and the drug.

However, information management in this field relies on fairly traditional
means, e.g. curated databases, which do not scale to (1) the rapid expansion
of the pharmacogenomics literature in recent years and (2) the increasingly
available volume of full text publications, which contain more specific and
(potentially) informative facts that MEDLINE abstracts.  Hence, although
there is a large demand and significant utility of text analytics to the
study of phamacogenomics, its potential is not fully realized; in part
because the work to date has failed to bridge the two distinct worlds--that
of (bench) molecular biology and that of (clinically oriented)
pharmacology--and because the developers of text analytics are not fully
aware of this challenging field.

Last year's workshop at PSB (Genotype-Phenotype-Drug relationship extraction
from text) examined the current state-of-the-art and reported ongoing
research of labs already involved in this area of research.  The steady
stream of work on extracting interactions from text, the increasing
attention in the Semantic Web towards capturing facts as
"nano-publications"(individual assertions that are attributable to authors
and traceable in their publications), and representing scientific discourse
in a structured manner, all indicate that the time seems to be ripe for
research that goes beyond the mere extraction of explicitly stated knowledge
in documents, to linking text-mined and database data through formal
reasoning to uncover implicit and in some sense "new" knowledge.

In order to advance this agenda, it is essential that existing relationship
extraction methods be compared to one another and that a community-wide
shareable benchmark corpus emerges against which such efforts can be
compared.  The goal of the workshop is to utilize a corpus put forth by
PharmGKB to compare different relationship extraction methods and the
corresponding "new" knowledge discovery they might drive.

This workshop aims to address the gap in coverage of text mining for
pharmacogenomics.  The technical area of the workshop is intended to
particularly focus on genotype-phenotype-drug relationships.  It will
include broad categories of work that have been well-studied in the past,
specifically text mining and reasoning, but will restrict submissions 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
* Associating gene variants (mutations, alleles, rs/ss numbers) to the
associated gene name
* Work on the corpus of documents linked to by PharmGKB
* Reasoning systems applied over the PharmGKB knowledge base

Work on named entity recognition (e.g. gene taggers) would not be considered
for inclusion.  Approaches that combine text-mining and knowledge-based
systems are of special interest.

ABSTRACTS

We are soliciting both research and position abstracts up to 500 words
related to the topics mentioned above.  The workshop will combine invited
talks, talks selected from abstract submissions in response to this call,
and a panel discussion.  Authors of all accepted abstracts will be invited
to submit full papers for publication in the Journal of Biomedical
Informatics.

Please submit abstracts to Udo.Hahn at uni-jena.de with the subject line "PSB
workshop submission".

The workshop website can be found at
http://psb.stanford.edu/workshop-textmining.html.

IMPORTANT DATES

Abstract deadline: August 31, 2010
Speaker notification: September 15, 2010
Workshop: TBA, but some time January 3-7 2011, during PSB

WORKSHOP ORGANIZERS

Kevin Bretonnel Cohen
Yael Garten
Udo Hahn
Nigam H. Shah


-- 
Kevin Bretonnel Cohen, PhD
Biomedical Text Mining Group Lead, Center for Computational Pharmacology, U.
Colorado School of Medicine
and
Lead Artificial Intelligence Engineer, The MITRE Corporation, Human Language
Technology Division
303-916-2417 (cell) 303-377-9194 (home)
http://compbio.uchsc.edu/Hunter_lab/Cohen
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