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BioTxtM 2012 : Third Workshop on Building and Evaluating Resources for Biomedical Text Mining


When May 26, 2012 - May 26, 2012
Where Istanbul, Turkey
Submission Deadline Feb 19, 2012
Notification Due Mar 14, 2012
Final Version Due Mar 28, 2012
Categories    text mining   corpus annotation   biomedical resources   domain adaptation

Call For Papers

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


** The workshop will feature an invited talk by Prof Jun'ichi Tsujii of Microsoft Research Asia, China **

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, 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

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 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:
National Centre for Text Mining, School of Computer Science, University of Manchester, UK

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