Appel: Workshop ACL: BioNLP 2007, Prague

Thierry Hamon thierry.hamon at LIPN.UNIV-PARIS13.FR
Fri Feb 2 20:14:23 UTC 2007

Date: Thu, 1 Feb 2007 10:06:16 +0100
From: Pierre Zweigenbaum <pz at>
Message-Id: <200702011006.17048.pz at>

[Cet atelier, associé à ACL 2007, sollicite des travaux sur les
 différents aspects du traitement automatique des langues
 appliqués aux domaines médical et biomédical.

		Pierre Zweigenbaum.]

Date: jeudi 1 février 2007 00:44:49
From: "Kevin B. Cohen" <kevin.cohen at>

BioNLP 2007

An ACL 2007 workshop
Prague, Czech Republic
June 29, 2007

Natural language processing has a long history in the medical domain,
with research in the field dating back to at least 1963.  In the late
1990s, a separate thread of research involving natural language
processing in the genomic domain began to gather steam. It has become
a major focus of research in the bioinformatics, computational
biology, and computational linguistics communities. A number of
successful workshops and conference sessions have resulted, with
significant progress in the areas of named entity recognition for a
wide range of key biomedical classes, concept normalization, and
system evaluation.  A variety of publicly available resources have
contributed to this progress, as well.

Recently, the widely recognized disconnect between basic biological
research and patient care delivery stimulated development of a new
branch of biomedical research--translational medicine. Translational
medicine, sometimes defined as the facilitation of "bench-to-bedside"
transmission of knowledge, has become a hot topic, with a National
Center for Biocomputing devoted to this theme established last year.

This workshop has the goal of addressing and bringing together these
three threads in biomedical natural language processing, or "BioNLP:"
biological, translational, and clinical language processing.  We will
solicit work in any topics of current interest in the field,

- Extraction and normalization of...
       - complex biomedical relations
       - biomedical entities, including experimental methodologies
- Resources for BioNLP, including....
       - ontologies
       - knowledge bases
       - lexicons
       - annotated data sets
       - corpora
- The economics of text mining for biomedical applications, including...
       - quantifying utility to end users
       - usability and portability for non-developers
- Novel strategies for system testing and evaluation, including...
       - evaluation methods
       - resources
       - test suites
- Applications and analysis techniques that use the output of text
mining systems...
      - knowledge discovery
      - integration of publications with databases
      - visualization

Two types of submissions are invited: full papers and poster
abstracts.  Submissions are due by 11:59pm EST on March 26,
2007. Submit your paper or abstract via the ACL BioNLP 2007 site at

Full papers should not exceed eight (8) pages including references.
These are intended to be reports of original and mature research.

Poster abstracts should not exceed two (2) pages. Accepted abstracts
will be published in a separate section of the workshop proceedings.
Appropriate poster topics include preliminary results, application
notes, descriptions of work in progress, etc.

Format: Submissions must be electronic and in PDF format, and should
follow the two-column format of ACL proceedings. Please see the
conference website for detailed typesetting specifications. Authors
are strongly encouraged to use the LaTeX or Microsoft Word style files
available on the ACL meeting website
( Authors who cannot submit a
PDF file electronically should contact the workshop organizers well in
advance of the submission deadline.

Reviewing of submissions will be blind. Do not include author names in
the paper. Avoid self-references -- instead of "As we showed in Smith
et al. 1999...", say "As Smith et al. 1999 showed...." The paper
submission software will allow you to enter full author information
separately from your paper. Each submission will be reviewed by at
least two program committee members.


Submissions due: March 26, 2007 (11:59 PM EST)
Notification of acceptance: April 27, 2007
Camera-ready papers due back from authors: May 2, 2007
Workshop: June 29, 2007


K. Bretonnel Cohen
Dina Demner-Fushman
Carol Friedman
Lynette Hirschman
John Pestian


Sophia Ananiadou
Lan Aronson
Breck Baldwin
Sabine Bergler
Olivier Bodenreider
Chris Brew
Bob Carpenter
Wendy Chapman
Aaron Cohen
Nigel Collier
Udo Hahn
Peter Haug
Marti Hearst
George Hripcsak
Steve Johnson
Michael Krauthammer
Alex Morgan
Serguei Pakhomov
Martha Palmer
Tom Rindflesch
Larry Smith
Lorrie Tanabe
Jun'ichi Tsujii
Alfonso Valencia
Karin Verspoor
Bonnie Webber
W. John Wilbur
Limsoon Wong
Hong Yu
Pierre Zweigenbaum

Please direct any questions to BioNLP2007 at gmail dot com.
Workshop URL:

Best wishes,

Kevin Bretonnel Cohen
Dina Demner-Fushman
Carol Friedman
Lynette Hirschman
John Pestian

K. B. Cohen
Biomedical Text Mining Group Lead
Center for Computational Pharmacology
303-916-2417 (cell) 303-377-9194 (home)

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