Appel: Third Workshop on Building and Evaluating Resources for Biomedical Text Mining, LREC 2012 Workshops

Thierry Hamon thierry.hamon at UNIV-PARIS13.FR
Sun Dec 18 13:30:34 UTC 2011

Date: Fri, 16 Dec 2011 18:14:06 +0100
From: ELRA ELDA Information <info at>
Message-ID: <4EEB7C5E.2070106 at>

[Apologies for cross-postings]

First Call for Papers

Saturday 26th May 2012
organised in conjunction with LREC2012 (21-27 May 2012, Lütfi Kirdar 
Istanbul Exhibition and Congress Centre, Turkey)

Over the past decade, biomedical text mining has received a large amount
of interest. Faced with the rapidly increasing volume of biomedical
literature, domain experts have an ever-increasing need for tools that
can help them locate isolate relevant nuggets of information from this
deluge of information in a timely and efficient manner. The response to
such issues by the natural language processing community can be clearly
evidenced in the biomedical natural language processing workshops that
have been held over that past 10 years, in conjunction with ACL or NAACL
meetings, to report the process in the field, as well as the founding of
an ACL special interest group.

Biomedical text mining applications are reliant on high quality
resources. These include databases and ontologies (e.g., Biothesaurus,
UMLS Metathesaurus, MeSH and the Gene Ontology) and
dictionaries/computational lexicons (e.g., the BioLexicon and the UMLS
SPECIALIST lexicon). Recent years have also evidenced a large increase
in the number of freely-available corpora (e.g., GENIA, GREC, AIMED,
BioInfer, CRAFT, BioDRB) annotated with an expanding range of
information types. These now include not only named entities and simple
relations that hold between them, but also more complex event structures
and coreference, as well as higher level information about how events
are to be interpreted (e.g., facts, analyses, speculations, etc.) and
discourse structure. Community shared tasks and challenges (e.g.,
JNLPBA, LL05, Biocreative I/II/III, BioNLP’09, BioNLP 2011, i2b2, etc.)
also normally involve the production of annotated corpora (on which the
participating systems are trained and evaluated) as well as helping to
steer research efforts to focus on open research problems.

Following on from the success of two previous workshops, the workshop
aims to bring together researchers who make use of biomedical text
mining resources such as the above in their applications, or who are
working on the development of new resources. The workshop will allow an
assessment of the current state of the art of resources, and will
provide a forum for the discussion of current problems, questions and
open issues, which will be useful in guiding further research in this
area. Such topics are very much relevant to META-NET (a Network of
Excellence consisting of 54 research centres from 33 countries), which
is dedicated to building the technological foundations of a multilingual
European information society. META-NET aims to push forward research to
allow a rapid expansion of language technologies; such efforts can only
be acheived if appropriate resources are available. Since META-NET is
concerned with enhancing information access for all European citizens,
submissions concerning biomedical resources for languages other than
English are particularly welcome. A further vital consideration to allow
rapid building of new applications is that of interoperability and
reuse. As a step towards this, several annotated corpora have been made
UIMA-compliant, and are available in the U-Compare system, which allows
easy construction of NLP workfows and evaluation against gold standard

Some specific questions that the workshop will aim to answer include the 

* Among the available resources, which are the most used? What makes a
  good resource? How can easily can resources be employed for different
  purposes? What efforts have been made to make resources reusable or
  interoperable? To what extent have these efforts been successful?

* Which resources are underused and why? What could be done to improve
  or extend them to improve their utility?

* Which types of resources are still lacking and what is needed
  urgently? Are any resources planned or in development to address such
  gaps? Are any resources available that cover languages other than

* To what extent do the existing resources support processing of text in
  different biomedical subdomains? How easily can they be adapted to
  deal with different domains?

We invite papers reporting on resources that facilitate biomedical text
mining, and the process of designing, building, updating, delivering,
using and evaluating them. The workshop will focus both on the lexical
and knowledge repositories themselves (e.g., terminologies, ontologies,
controlled vocabularies, factual databases, annotated corpora, etc.) as
well as on issues relating to their usability (e.g., design guidelines,
standards for building resources, storage and exchange formats,
interoperability issues, etc).

Topics of interest include but are not limited to:

* Building biomedical resources: controlled vocabularies, terminologies,
  ontologies, corpora
* Guidelines and annotation schemas, tools, challenges, interoperability
* Reengineering existing biomedical or general language resources
* Update, evolution, extension or enrichment of resources
* Adapting resources to new sub-domains
* Interoperability of resources and standards
* Lightly annotated and noisy resources
* Tools for exploration of resources
* Data exchange formats
* Evaluation, comparison and critical assessment of resources /
  evaluation metrics
* Test suites


*Sophia Ananiadou, National Centre for Text Mining, University of 
 Manchester, UK
*Kevin Bretonnel Cohen, Computational Bioscience Program, University of 
 Colorado School of Medicine, USA
*Dina Demner-Fushman, National Library of Medicine, USA
*Paul Thompson, National Centre for Text Mining, University of 
 Manchester, UK

February 10, 2012 Paper submissions due
March 14, 2012 Paper notification of acceptance
March 28, 2012 Camera-ready papers due
May 26, 2012 Workshop

Papers must describe original, completed or in progress, and unpublished
work. Each submission will be reviewed by two program committee members.
Accepted papers will be given up to 8 pages in the workshop proceedings,
and will be presented either as an oral presentation or poster.

Papers should be formatted according to the stylesheet, which will be
provided on the LREC 2012 website (

Please submit papers in PDF format to:

Paper review will be blind, so papers should not include authors' names
and affiliations.
Accepted papers will be published in the workshop proceedings.

When submitting a paper through the START page, authors will be kindly
asked to provide relevant information about the resources that have been
used for the work described in their paper or that are the outcome of
their research. For further information on this initiative, please refer
to Authors will also be
asked to contribute to the Language Library, the new initiative of


Jari Björne, University of Turku, Finland
Olivier Bodenreider, National Library of Medicine, USA
Wendy Chapman, University of Pittsburgh, USA
Hongfang Liu, Mayo Clinic, USA
Naoaki Okazaki, Tohoku University, Japan
Sampo Pyysalo, University of Manchester, UK
Andrey Rzhetsky, University of Chicago, USA
Stefan Schulz, Medical University Graz, Austria
Lucy Vanderwende, Microsoft, USA
Karin Verspoor, NICTA, Australia
John Wilbur, NCBI, NLM, NIH, USA
Stephen Wu, Mayo Clinic, USA
Pierre Zweigenbaum, LIMSI, France

Workshop contact person:
Paul.Thompson at
National Centre for Text Mining, School of Computer Science, University
of Manchester, UK

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