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Thu Mar 25 16:49:58 UTC 2004


COLING Workshop


Call for Papers

Geneva, Switzerland
August 28-29, 2004

** Regular papers deadline: 14th April **
** Shared task paper deadline: 21st April **

Workshop Description

Recent years have seen a growing interest in the application of NLP
techniques to texts in the domains of biology and medicine. The
problem of information overload that has resulted from the massive
growth in the scientific literature has clearly shown the necessity to
automatically locate, organize and manage facts relating to
experimental results.  At the same time clinicians have experienced
greatly improved access to the medical literature and clinical
repositories which needs to be matched by the development of enhanced
information access tools. This year NLPBA
( and BioNLP
( merge for a
joint workshop with the aim of bringing together researchers from
natural language processing, bio-informatics, medicine and ontologies
who are concerned with developing methods and resources for solving
these problems.

Over the last five years we have seen significant steps forward in the
development of language technology and large-scale resources for the
Bio-Medical domain such as linguistically annotated corpora
(e.g. GENIA POS and NE corpora), ontologies (e.g. Gene Ontology),
thesauri (e.g. UMLS Metathesaurus), lexicons and term lists (e.g. UMLS
SPECIALIST) as well as information retrieval collections (e.g. TREC
Genomics track). At the application level we see development of
question answering systems, event recognition, zone (rhetorical
region) identification, as well as term and bio-entity
recognition. The demand for information access tools from domain users
is increasing to support literature survey, often integrated into
online portals where scientists can navigate through related
information resources such as genetics and disease databases.  Ongoing
challenges relate to the growing and ambiguous nomenclature, the need
to integrate deep knowledge sources into machine learning, a need to
scale up methods for processing full text articles etc.

The objective of the workshop is to bring together researchers in this
area, to establish common themes and goals between different
groups. We have seen from previous experience in the natural language
learning and information retrieval communities the benefits of sharing
resources and developing common evaluation criteria. In this workshop
we are introducing a special shared task to promote discussion of
these issues as well as the objective of integrating machine learning
with knowledge resources.

We invite submission of papers on topics related to bio-medical NLP
including, but not limited to:

* Information extraction
* Text mining
* Named entity recognition
* Coreference resolution
* Term recognition
* Knowledge-based information retrieval
* Multi-lingual resources and applications
* Ontology construction and ontology mapping
* Visualization tools for viewing clustered or extracted information or
* Multi-modal approaches combining text and images, etc.
* Event recognition
* Construction of pathways from literature and databases
* Creation of data-sets of bio-medical entities, coreferences and relations
* Annotation standards and quality control methodologies
* Resource integration and re-engineering
* Corpus/lexicon construction
* Text summarization and report generation

Shared Task

This year we propose to have a special shared task: bio-medical named
entity recognition from the GENIA corpus. The purpose of this track is
essentially to investigate the integration of statistical machine
learning methods with symbolic knowledge sources from the bio-medical
domain such as ontologies, thesauri and lexicons : shared task

Invited Speaker

To be announced soon

Paper Format and Submission

Papers must follow the COLING 2004 templates, and will be submitted by
email to jnlpba-submit at Regular papers should follow the
COLING 2004 templates for regular papers (i.e. at most 7 pages) and
shared task papers should be formatted as per the COLING project notes
style (4 pages) focussing in particular on method, results and

Important Dates
Submission deadline for regular workshop papers:  April 14th, 2004
Submission deadline for shared task papers: April 21st, 2004
Notification of accepted papers:  May 14th, 2004
Deadline for camera ready copies: June 6th, 2004

Workshop Chairs
Nigel Collier (National Institute of Informatics, Japan)
Patrick Ruch  (University Hospital of Geneva and EPFL, Switzerland)
Adeline Nazarenko (LIPN, France)

Organizing Committee
Alfonso Valencia (Centro Nacional de Biotecnologia, Spain)
Carol Friedman (CUNY/Columbia University, USA)
Donia Scott (University of Brighton, UK)
Udo Hahn (Albert-Ludwigs University, Freiburg, Germany)
Junichi Tsujii (University of Tokyo, Japan)

Program Committee
Sophia Ananiadou (University of Salford, UK)
Alan Aronson (National Library of Medicine, USA)
Robert Baud (University Hospital of Geneva, Switzerland)
Christian Blaschke (CNB, Spain)
Oliver Bodenreider (National Library of Medicine, USA)
Berry de Bruijn (National Research Center, Canada)
Marc Craven (University of Wisconsin, USA)
Robert Gaizauskas (University of Sheffield, UK)
Eric Gaussier (Xerox, XRCE, France)
Vasileios Hatzivassiloglou (Columbia University, USA)
Lynette Hirschman (MITRE, USA)
Dimitar Hristovski (University of Ljubljana, Slovenia)
Jerry Hobbs (USC/ISI, USA)
Aravind Joshi  (University of Pennsylvania, USA)
Su Jian (Institute for Infocomm Research, Singapore)
Asao Fujiyama (National Institute of Informatics, Japan)
Arne Jonsson (University of Linkoping, Sweden)
Frederique Lisacek (GeneBio SA, Switzerland)
Yuji Matsumoto (NAIST, Japan)
Claire Nedellec (INRA, France)
Kousaku Okubo (Kyushu University, Japan)
Jong C. Park (KAIST, Korea)
Thierry Poibeau (LIPN, France)
Denys Proux (Xerox, XRCE, France)
James Pustejovsky (Brandeis University, USA)
Dietrich Rebholz-Schuhmann (European Bioinformatics Institute, EU)
Irena Spasic  (UMIST, UK)
Ben Stapley (UMIST, UK)
Padmini Srinivasan (University of Iowa, USA)
Hirotoshi Taira (NTT Communication Science, Japan)
Toshihisa Takagi (University of Tokyo, Japan)
Yuka Tateishi (University of Tokyo, Japan)
Anne-Lise Veuthey (SIB, Switzerland)
Limsoon Wong (Institute for Infocomm Research, Singapore)
Pierre Zweigenbaum (AP-HP, INSERM & INaLCO, France)

Shared Task Committee
Nigel Collier (National Institute of Informatics, Japan)
Jindong Kim (University of Tokyo, Japan)
Yuka Tateisi (University of Tokyo, Japan)
Tomoko Ohta (University of Tokyo, Japan)
Yoshimasa Tsuruoka (University of Tokyo, Japan)

Contact Information

General organization : jnlpba-request at
Shared task organization: bio04sharedtask at
Main page :

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