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Subject: [ E-CFP ] Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (LREC2012)
From: <Paul.Thompson_(on)_manchester.ac.uk>
Date received: 20 Dec 2011
Deadline: 10 Feb 2012
Start date: 26 May 2012

First Call for Papers

BIOMEDICAL TEXT MINING 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 corpora.

Some specific questions that the workshop will aim to answer
include the following:
* 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 English?
* 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,
* 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

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

SUBMISSIONS 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
http://www.lrec-conf.org/lrec2012/?LRE-Map-2012. Authors will
also be asked to contribute to the Language Library, the new
initiative of LREC2012.


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)_manchester.ac.uk National
Centre for Text Mining, School of Computer Science, University of
Manchester, UK


Paul Thompson Research Associate School of Computer Science
National Centre for Text Mining Manchester Interdisciplinary
Biocentre University of Manchester 131 Princess Street Manchester
M1 7DN UK Tel: 0161 306 3091


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