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BioNLP 2011 : ACL BioNLP workshop


When Jun 23, 2011 - Jun 24, 2011
Where Portland, Orgeon
Submission Deadline Mar 29, 2011
Notification Due Apr 25, 2011
Final Version Due May 2, 2011
Categories    text mining   natural language processing   bioinformatics

Call For Papers

Call For Papers

BioNLP 2011
June 23-24, 2011, Portland, Oregon


Over the course of the past nine years, the ACL BioNLP workshop has
established itself as the primary venue for presenting foundational
research in language processing for the biological and medical
domains. The workshop serves as both a venue for bringing together
researchers in bio- and clinical NLP, and a venue for informing
mainstream ACL researchers about this fast-growing and important
domain. This year will be the tenth year that the workshop has been
held in association with the annual ACL or NAACL meeting and the third
year that the workshop is associated with the new SIGBIOMED special
interest group. in accordance with the ACL SIGBIOMED
( tradition of presenting work on a broad range of
topics, we invite submissions on any topic of current interest in the
field of Biomedical Natural Language Processing. Topics especially
encouraged include:

* Implemented and integrated BioNLP systems
* Entity identification and normalization for a broad range of
semantic categories
* Extraction of complex relations
* Discourse analysis
* Anaphora and coreference resolution
* Text mining
* Summarization
* Translation of clinical data for patients
* Question Answering
* Resources and novel strategies for system testing and evaluation
* Computational analysis of linguistic correlates of biomedical conditions


Two types of submissions are invited: full papers and poster
abstracts. Submissions are due by 11:59 PM EST on Friday, April 1,
2011. Submit your paper or abstract via the START website:

Full papers should not exceed eight (8) pages of text and two pages of
references. These are intended to be reports of original research.
BioNLP aims to be the forum for interesting, innovative, and promising
work involving biomedicine and language technology, whether or not
yielding high performance at the moment. This by no means precludes
our interest in and preference for mature results, strong performance,
and thorough evaluation. Both types of research and combinations
thereof are encouraged.

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.

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 style files and formatting instructions
available on the ACL/HLT conference website: (scroll down)

Submissions need to be anonymous. Authors who cannot submit a PDF file
electronically should contact the workshop organizers well in advance
of the submission deadline.

Dual submission policy: note that papers may not be submitted to the
BioNLP 2011 workshop if they are or will be concurrently submitted to
another meeting or publication and that other meeting or publication
prohibits dual submissions. If your paper is also submitted to ISMB or
AMIA, you should expect it to be rejected by ISMB and AMIA. If your
paper is or will be concurrently under consideration by another
meeting or publication, notify us of that fact in a footnote on the
first page. Do not dual-submit your BioNLP 2011 workshop paper to ISMB
or AMIA.


Submissions for papers on the shared task are being handled
separately. For more information on shared task paper submissions, see


ACL is providing a mentoring (coaching) service for authors from
regions of the world where English is less emphasized as a language of
scientific exchange. Many authors from these regions, although able to
read the scientific literature in English, have little or no
experience in writing papers in English for conferences such as the
ACL meetings. The service will be arranged as follows. A set of
potential mentors will be identified by Mentoring Service Chair Tim
Baldwin (U. Melbourne), who will organize this service for ACL/HLT
2011. If you would like to take advantage of the service for a
submission to this workshop, please upload your paper in PDF format
using the paper submission software for the mentoring service
available at:

The deadline for the mentoring service is six weeks before the
workshop submission deadline. An appropriate mentor will be assigned
to your paper and the mentor will get back to you no later than two
weeks before the submission deadline.

Please note that this service is for the benefit of the authors as
described above. It is not a general mentoring service for authors to
improve the technical content of their papers.

Questions about the mentoring service should be referred to tb at


March 29, 2011: Submission deadline
April 25, 2011: Notification of acceptance
May 2, 2011: Camera-ready copy due from authors
June 23-24: Workshop


The organizing committee for BioNLP 2011 is:

* Kevin Bretonnel Cohen, Center for Computational Pharmacology,
University of Colorado School of Medicine and The MITRE Corporation
* Dina Demner-Fushman, Lister Hill National Center for Biomedical
* Sophia Ananiadou, University of Manchester and UK National
Centre for Text Mining
* John Pestian, Computational Medicine Center, University of
Cincinnati, Cincinnati Children's Hospital Medical Center
* Jun'ichi Tsujii, U. Tokyo and UK National Centre for Text Mining
* Bonnie Webber, U. Edinburgh

The program committee for BioNLP 2011 comprises a strong set of BioNLP
researchers from North America, Europe, and Asia:

* Alan Aronson, LHNCBC, US National Library of Medicine
* Catherine Blake, University of North Carolina
* Olivier Bodenreider, LHNCBC, US National Library of Medicine
* Wendy Chapman, University of Pittsburgh
* Aaron Cohen, Oregon Health and Science University
* Nigel Collier, National Institute of Informatics, Tokyo
* Noemie Elhadad, Columbia University
* Marcelo Fiszman, US National Library of Medicine
* Kristofer Franzén, Swedish Institute of Computer Science
* Filip Ginter, University of Turku, Finland
* Su Jian, A-star
* Jin-Dong Kim, University of Tokyo
* Marc Light, Thomson
* Zhiyong Lu, NCBI, US National Library of Medicine
* Aurelie Neveol, US National Library of Medicine
* Serguei Pakhomov, University of Minnesota
* Sampo Pyysalo, University of Tokyo, Japan
* Thomas Rindflesch, LHNCBC, US National Library of Medicine
* Brian Roark, Oregon Graduate Institute
* Daniel Rubin, Stanford University
* Andrey Rzhetsky, U. Chicago
* Hagit Shatkay, Queen's University, Canada
* Larry Smith, NCBI, US National Library of Medicine
* Yuka Tateisi, Kogakuin University, Japan
* Yoshimasa Tsuruoka, JAIST, Japan
* Alfonso Valencia, Centro Nacional de Biotecnologia
* Karin Verspoor, University of Colorado School of Medicine
* Xinglong Wang, UK National Centre for Text Mining
* Peter White, Children's Hospital of Philadelphia
* W. John Wilbur, NCBI, US National Library of Medicine
* Limsoon Wong, National University of Singapore
* Hong Yu, University of Wisconsin
* Pierre Zweigenbaum, LIMSI

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