BioNLP 2007
A workshop of ACL 2007
Prague, Czech Republic
E-mail: BioNLP2007 at googlegroups dot com

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Call for Papers

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, especially:

  • 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, Center for Computational Pharmacology, University of Colorado School of Medicine
Dina Demner-Fushman, Lister Hill National Center for Biomedical Communications
Carol Friedman, Department of Biomedical Informatics, Columbia University
Lynette Hirschman, Biomedical Informatics, MITRE
John Pestian, Computational Medicine Center, University of Cincinnati, Cincinnati Children's Hospital Medical Center


  • Sophia Ananiadou, NaCTeM
  • Lan Aronson, NLM
  • Breck Baldwin, alias-i
  • Sabine Bergler, Concordia University
  • Christian Blaschke, bioalma
  • Olivier Bodenreider, NLM
  • Chris Brew, Ohio State University
  • Bob Carpenter, alias-i
  • Wendy Chapman, University of Pittsburgh
  • Aaron Cohen, Oregon Health and Science University
  • Nigel Collier, National Institute of Informatics
  • Udo Hahn, JULIE Lab, Jena University
  • Peter Haug, University of Utah
  • Marti Hearst, UC Berkeley
  • George Hripcsak, Columbia University
  • Steve Johnson, Columbia University
  • Michael Krauthammer, Yale
  • Alex Morgan, Stanford
  • Serguei Pakhomov, Mayo Clinic
  • Martha Palmer, University of Colorado at Boulder
  • Tom Rindflesch, NLM
  • Hagit Shatkay, Queens University
  • Larry Smith, NLM
  • Lorrie Tanabe, NLM
  • Jun'ichi Tsujii, University of Tokyo and NaCTeM
  • Alfonso Valencia, CNIO
  • Karin Verspoor, Los Alamos National Laboratory
  • Bonnie Webber, University of Edinburgh
  • W. John Wilbur, NLM
  • Limsoon Wong, National University of Singapore
  • Hong Yu, University of Wisconsin
  • Pierre Zweigenbaum, LIMSI

Best wishes,

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

Please direct any questions to BioNLP2007 at googlegroups dot com.

This document last modified 08/09/10 13:08.