Appel: COLING 2004 : NLP in Biomedicine and its Applications

alexis.nasr at LINGUIST.JUSSIEU.FR alexis.nasr at LINGUIST.JUSSIEU.FR
Fri Feb 27 14:23:47 UTC 2004


COLING Workshop

International Joint Workshop on Natural Language Processing
in Biomedicine and its Applications


Call for Papers

Geneva, Switzerland
August 28-29, 2004

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 description.

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

Important Dates
Submission deadline for workshop papers:  April 14th, 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)

Contact Information

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


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