Appel: Call for Chapters in IR in Biomedicine: NLP and Knowledge Integration

Thierry Hamon thierry.hamon at LIPN.UNIV-PARIS13.FR
Fri Aug 24 13:01:24 UTC 2007

Date: Fri, 24 Aug 2007 11:48:00 +0200
From: Violaine PRINCE <prince at>
Message-Id: <4e51908f256cf3041f4c6d5ad7efa237 at>

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
processing. 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 hybridation 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

Innovative Software in BioNLP (short papers)


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,, 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 00
E-mail: prince at

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