21.2784, Calls: Computational Linguistics/USA

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LINGUIST List: Vol-21-2784. Fri Jul 02 2010. ISSN: 1068 - 4875.

Subject: 21.2784, Calls: Computational Linguistics/USA

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1)
Date: 22-Jun-2010
From: Kevin Cohen < kevin.cohen at gmail.com >
Subject: Mining the Pharmacogenomics Literature
 

	
-------------------------Message 1 ---------------------------------- 
Date: Fri, 02 Jul 2010 12:54:41
From: Kevin Cohen [kevin.cohen at gmail.com]
Subject: Mining the Pharmacogenomics Literature

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Full Title: Mining the Pharmacogenomics Literature 

Date: 03-Jan-2011 - 07-Jan-2011
Location: Kona, Hawaii, USA 
Contact Person: Kevin Bretonnel Cohen
Meeting Email: kevin.cohen at gmail.com
Web Site: http://psb.stanford.edu/workshop-textmining.html 

Linguistic Field(s): Computational Linguistics 

Call Deadline: 31-Aug-2010 

Meeting Description:

The aim of this workshop is to bring together researchers working on the
automatic or semi-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 the use of the relationships for advancing
pharmacogenomic research. Efforts aimed at creating benchmark corpora as well as
comparative evaluation of existing relationship extraction methods are of
special interest. 

Call for Papers

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 than Medline abstracts. Hence, although there is
a large demand and significant utility of text analytics to the study of
pharmacogenomics, 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 thedevelopers
of text analytics are not fully aware of this challenging field.

Last year's workshop (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 even 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 sharable
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 to this call, and a panel discussion.
Submitted abstracts that will be reviewed by the co-chairs for selecting
submitted talks. Authors of all accepted abstracts will be invited to submit
full papers for publication in a yet-to-be-determined journal.
 
Please submit abstracts to Udo.Hahn at uni-jena.de with the subject line PSB
workshop submission.

Important Dates:

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

Workshop Organizers:

Kevin Bretonnel Cohen
Yael Garten
Udo Hahn
Nigam H. Shah





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