[Elsnet-list] Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (LREC2012): Call for Participation

Paul Thompson Paul.Thompson at manchester.ac.uk
Tue Apr 10 12:41:50 CEST 2012

First call for participation

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


Registration: http://confreg.elda.org/


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, LLl05, 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. 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.

Invited Talk

* Jun'ichi Tsujii, Microsoft Research Asia
 Semantic and Linguistic Annotations in GENIA


 * Claudiu Mihăilă, Riza Theresa Batista-Navarro, Sophia Ananiadou
 Analysing Entity Type Variation across Biomedical Subdomains

* Suwisa Kaewphan, Sanna Kreula, Sofie Van Landeghem, Yves Van de Peer, Patrik R. Jones and Filip Ginter
 Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP(H) Metabolism in E. coli with Event Extraction

* Mariana Neves, Alexander Damaschun, Andreas Kurtz and Ulf Leser
 Annotating and Evaluating Text for Stem Cell Research

* Raheel Nawaz, Paul Thompson and Sophia Ananiadou
 Meta-Knowledge Annotation at the Event Level: Comparison between Abstracts and Full Papers

* Fei Xia and Meliha Yetisgen-Yildiz
 Clinical Corpus Annotation: Challenges and Strategies

*Dimitrios Kokkinakis
 The Journal of the Swedish Medical Association - a Corpus Resource for Biomedical Text Mining in Swedish

* Philippe Thomas, Tamara Bobić, Martin Hofmann-Apitius, Ulf Leser and Roman Klinger
 Weakly Labeled Corpora as Silver Standard for Drug-Drug and Protein-Protein Interaction

*Amber Stubbs
 Developing Specifications for Light Annotation Tasks in the Biomedical Domain


*Hercules Dalianis and Henrik Boström
 Releasing a Swedish Clinical Corpus after Removing All Words - De-Identification Experiments with Conditional Random Fields and Random Forests

*Alyaa Alfalahi, Sara Brissman and Hercules Dalianis
 Pseudonymisation of Personal Names and other PHIs in an Annotated Clinical Swedish Corpus

*Olfa Makkaoui, Julien Desclés and Jean-Pierre Desclés
 Evaluation and Performance Improvement of the BioExcom System for the Automatic Detection of Speculation in Biomedical Texts


*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


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<mailto: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
M1 7DN
Tel: 0161 306 3091

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