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LINGUIST List 18.2568

Mon Sep 03 2007

FYI: Call for Chapters in IR in Biomedicine

Editor for this issue: Fatemeh Abdollahi <fatemehlinguistlist.org>

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        1.    Mathieu Roche, Call for Chapters in IR in Biomedicine

Message 1: Call for Chapters in IR in Biomedicine
Date: 31-Aug-2007
From: Mathieu Roche <Mathieu.Rochelirmm.fr>
Subject: Call for Chapters in IR in Biomedicine
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Call for Chapters

Submission Deadline: November 1, 2007
Information Retrieval in Biomedicine: Natural Language Processing for
Knowledge Integration
A book edited by Pr. Violaine Prince and Dr Mathieu Roche, University of
Montpellier and LIRMM-CNRS, France


There is nowadays an intense interest for bio natural language
This field addresses the particular applications of natural language
processing (NLP) to biological and medical areas. Naming such a set of
applications denotes both the impact of NLP on the application domain. As
a feedback, the peculiarities of the later seems to have made NLP evolve in
a distinct and particular way.

Several articles and books chapters have been recently written on the
subject (Ibekwe-Sanjuan 2007, Ananiadou and McNaught 2006, Scherf
et al. 2005, Cohen and Hersh 2005 are among the latest...). The issue they
tackle rises from the intensive research and publication activity in the
medical area. A bibliographical database such as Medline contains several
millions of articles and is thoroughly updated every day. Many medical
researchers and practitioners need to read papers not only in their
discipline but in other fields with which they have an interaction. For
instance, cancer specialists need to browse papers in oncogenetics,
radiology, chemistry, cellular biology, surgery and so forth. Every day new
cross-studies are published, and the medical community cannot cope with
such a high rate of information without being supported by automated or
semi-automated tools in Information Retrieval and Knowledge Integration.

According to Swanson's pioneer work in the domain (Swanson 1986),
the abundant medical data could be used as a hypothesis generator for
orienting medical research. Since human operators cannot browse the
huge amount of information, he suggested that hidden correlations could be
automatically or semi-automatically found in this data, so as to suggest
new tracks for investigation. Nowadays, the most recent works in text
mining are able to suggest this type of scientific discovery: A recent work
by Chun et al. (2006) shows that mining Medline abstracts brought up
interesting topical relations between prostate cancer and genes. Beyond
medicine, it is the whole field of the ''living sciences'', including all
facets of biology, that might benefit from text mining methods and
achievements (A recent paper by Ananiadou et al. (2006) describes
perspective actions of text mining in systems biology).

The Overall Objective of the Book

In the fields of bio NLP there exists a need for an edited collection of
articles in this area. Until now, the most intensively explored NLP areas
in biomedicine are those related to lexical knowledge and terminology.
Named entities recognition, abbreviations understanding and expansion,
terminological knowledge management have been largely addressed, with more
or less success. However, since NLP parsers are becoming more
efficient, and word-based approaches have reached their limits, new trends,
suggesting hybridization between linguistic knowledge and machine
learning or statistics-based algorithms are being seriously investigated.

The book aims to provide relevant theoretical frameworks and latest
empirical research findings in the area, according to a linguistic
granularity. At the lexical and terminological levels, it aims at
presenting original applications, going beyond the existing published work.
At the sentence level, it should present the latest achievements,
particularly by using NLP parsers. At the text/paragraph level, it is the
relationship with topics and pragmatics that opens the road for a broader
use of NLP in biomedicine. Moreover, two chapters will focus on aspects of
NLP which are becoming crucial: Evaluation and Innovative Software.

The Target Audience:

Professionals, PhD students and researchers working in the field of
Text Mining, BioNLP, Medical Sciences, and Computer-Assisted Medical
information systems. It is also relevant for computational linguists and
linguists who want to solve particular problems brought out by the
application domain. Moreover, the book will provide insights and support
executives concerned with the management of expertise, knowledge, and
information in health systems and biological textbases.

Recommended topics include the following:

Lexical-terminological level: Lexicology and terminology in BioNLP ;
Using Bio ontologies within a language context ; Updating ontologies in
biology or medicine with lexical knowledge

Sentence level: The question-answer approach in biomedicine;
Operative knowledge derived from NLP parsing and/or semantic representation
(application to biology and/or medicine); Approaches linking sentence level
with either terminology or segment level

Segment level: A topical and topic change approach to BioNLP (for
Information Retrieval or Knowledge Integration); Rhetorical structures,
scripts, or other models of this granularity; Approaches involving language
pragmatics in Biomedicine

Evaluation: Models or points of view in evaluating NLP approaches
to biomedicine

Innovative Software in BioNLP (short papers)

Submission Procedure

Researchers and practitioners are invited to submit on or before
November 1, 2007, a 2-5 page manuscript proposal clearly explaining the
mission and concerns of the proposed chapter. Authors of accepted proposals
will be notified by December 1, 2007 about the status of their proposals
and sent chapter organizational guidelines. Full chapters are expected to
be submitted by March 15, 2008. All submitted chapters will be reviewed on
a double-blind review basis. The book is scheduled to be published by IGI
Global, www.igi-pub.com, publisher of the IGI Publishing (formerly Idea
Group Publishing), Information Science Publishing, IRM Press, CyberTech
Publishing and Information Science Reference (formerly Idea Group
Reference) imprints.

Inquiries and submissions can be forwarded electronically (Word
document) or by mail to:
Pr Violaine Prince
University of Montpellier 2 and LIRMM-CNRS
161 Ada Street F34392 Montpellier cedex 5
Tel.: +334 67 41 86 74 Fax: +334 67 41 85 00 GSM: +336 07 34 01
E-mail: princelirmm.fr

Linguistic Field(s): General Linguistics

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