2nd Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM)


Tuesday 18th May, 2010

Mediterranean Conference Centre in Valletta, Malta

The 2nd workshop on Building and Evaluating Resources for Biomedical Text Mining will be held at LREC 2010, Malta on Tuesday 18th May 2010.

Biomedical text mining over the last decade has become one of the driving application areas for the NLP community, resulting in a series of very successful yearly specialist workshops at ACL since 2002, BioNLP, as well as the launch of the BioMed special interest group in 2008.

In the past, most of the work has focused on solving specific problems, often using task-tailored and private data sets. This data was rarely reused, in particular outside the efforts of the providers. This has changed during the last years, as many research groups have made available resources that have been built either purposely or as by-products of research or evaluation efforts. A number of projects, initiatives and organisations have been dedicated to building and providing biomedical text mining resources (e.g., the GENIA suite of corpora, PennBioIE, TREC Genomics track, BioCreative, Yapex, LLL05, BOOTStrep, JNLPBA, KDD data, Medstract, BioText, etc.). There is an increasing need to provide community-wide discussions on the design, availability and interoperability of resources for bio-text mining, following on from specific applications such as gene name identification and protein-protein interactions in BioCreative I/II, the BioNLP'09 shared task on event extraction etc., and recognition of clinically relevant entities and relations in the i2b2 challenges to the use of common resources and tools in real life applications.

The papers accepted for presentation at the workshop reflect the current transitional state of the biomedical text mining field. The biomedical text mining field is expanding in two directions: enrichment and use of cross-lingual resources and work in resource-poor languages on the one hand, and significant inroads in processing clinical narrative on the other hand.

In addition to the accepted papers, there will be talks from 2 invited speakers:

  • Pierre Zweigenbaum, Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur (LIMSI-CNRS), France
  • Simonetta Montemagni, Istituto di Linguistica Computazionale (ILC-CNR), Italy

The complete programme for the workshop can be found here:

Registration for the workshop, as well as the main LREC conference, is available here.


  • Sophia Ananiadou, National Centre for Text Mining, University of Manchester
  • Kevin Bretonnel Cohen, Center for Computational Pharmacology, The MITRE Corporation
  • Dina Demner-Fushman, National Library of Medicine


  • Olivier Bodenreider, National Library of Medicine, USA
  • Wendy Chapman, University of Pittsburgh, USA
  • Aaron Cohen, Oregon Health and Science University
  • Liu Hong Fang, Georgetown University Medical Center, USA
  • Martin Krallinger, National Biotechnology Center, Spain
  • John McNaught, University of Manchester, UK
  • John Pestian, Computational Medicine Center, University of Cincinnati, USA
  • Andrey Rzhetsky, University of Chicago, USA
  • Jian Su, Institute for Infocomm Research, Singapore
  • Junichi Tsujii, University of Tokyo, Japan and National Centre for Text Mining, UK
  • Yoshimasa Tsuruoka, JAIST, Japan
  • Karin Verspoor, Center for Computational Pharmacology, University of Colorado, USA
  • Xinglong Wang, University of Manchester, UK
  • Bonnie Webber, University of Edinburgh, UK
  • John Wilbur, NCBI, NLM, NIH, 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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