[Corpora-List] Final CALL FOR PARTICIPATION: Fifth BioCreative Challenge workshop

Martin Krallinger mkrallinger at cnio.es
Tue Sep 1 19:00:29 CEST 2015


**************************************************************** **************************************************************** Fifth BioCreative Challenge workshop, Seville, Spain

Home page: http://www.biocreative2015.org

Challenge tasks: http://www.biocreative.org/events/biocreative-v/CFP

Workshop date: 9-11th Sept 2015

Workshop format: Keynote speech, paper presentations, poster and group discussions.

With currently over 80 registered participants we foresee that the Fifth BioCreative Challenge workshop will be the most significant event in the field of biomedical text mining this year.

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[Apologies for multiple postings]

*********** 1. SCOPE *********** BioCreative: Critical Assessment of Information Extraction in Biology is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain.

Built on the success of the previous BioCreative Challenge Evaluations and Workshops (BioCreative I, II, II.5, III, 2012 workshop, and IV), the BioCreative Organizing Committee will host the BioCreative V Challenge in Sevilla, Spain on September 9-11, 2015.

*********** 2. TOPICS *********** This workshop invites proceedings papers and posters of teams participating in the BioCreative V tracks. Additionally we invite also posters on other topics related to biomedical text mining, information retrieval and natural language processing. Topics of interest include:

* Demonstration of real world cases of crowdsourcing and community annotations for generating Gold Standard annotations for text mining and database annotations * Use of text mining strategies to extract clinically relevant information from public data and clinical records, with a special focus on disease and symptom related concepts.

* The importance and practical use of text mining and information extraction systems for the extraction of biological and biomedical annotations and integration to existing life sciences knowledgebases * Named entity recognition of chemical compounds and gene/protein mentions in patents * Development and integration of BioC compatible modules that assist interaction database curation * Automatic detection of chemical/drugs and diseases, and their relations in PubMed abstracts

* Text mining solutions to develop and test novel approaches for relation extraction in the context of pathway networks

* Demonstration and evaluation of web-based systems addressing user-defined tasks, evaluated by curators on performance and usability

* Demonstration of tools to extract metagenomics metadata, including environment and habitat metadata

Authors can submit short proceedings papers and posters describing systems participating in BioCreative V tracks. Additionally we invite also posters on other topics related to biomedical text mining, information retrieval and natural language processing. Proceedings authors will be invited to submit full papers for a special journal issue. Previous special issues: http://www.biocreative.org/resources/publications

*********** 3. DATES *********** * Workshop date: 9-11th September 2015 * For track-related deadlines: check timelines: http://www.biocreative.org/events/biocreative-v/CFP * Late registration: After Aug 25, see

http://www.biocreative2015.org/registration/register-information

*********** 4. KEYNOTES *********** * Prof. Ioannis Xenarios (Center for Integrative Genomics - University of Lausanne; Vital-IT, SIB) * Prof. Søren Brunak (University of Copenhagen; Technical University of Denmark)

*********** 5. CONFIRMED PANELISTS *********** Sophia Ananiadou, University of Manchester / NaCTeM Jo McEntyre, Europe PubMed Central / EMBL-EBI Thomas Lemberger, EMBO Natalie Cattlet, Selventa Shawn Polson, University of Delaware Ioannis Xenarios, Swiss Bioinformatics Institute Lynette Hirschman, The MITRE Corporation Karën Fort, University Paris-Sorbonne Stéphanie Boué, PMI Lynn Schriml, Institute for Genome Sciences, University of Maryland Laura I. Furlong, GRIB – IMIM Juliane Fluck, Fraunhofer Institute SCAI

*********** 6. BIOCREATIVE ORGANIZING COMMITTEE *********** Cecilia Arighi, University of Delaware, USA Kevin Cohen, University of Colorado, USA Donald Comeau, National Center for Biotechnology Information (NCBI), NIH, USA Juliane Fluck, Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Germany Rezarta Islamaj Dogan, National Center for Biotechnology Information (NCBI), NIH, USA Lynette Hirschman, MITRE Corporation, USA Sun Kim, National Center for Biotechnology Information (NCBI), NIH, USA Martin Krallinger, Spanish National Cancer Centre, CNIO, Spain Zhiyong Lu, National Center for Biotechnology Information (NCBI), NIH, USA Fabio Rinaldi, Institute of Computational Linguistics, University of Zurich, Switzerland Alfonso Valencia, Spanish National Cancer Centre, CNIO, Spain Thomas Wiegers, North Carolina State University, USA John Wilbur, National Center for Biotechnology Information (NCBI), NIH, USA Cathy Wu, University of Delaware and Georgetown University, USA

Martin Krallinger, On behalf of the BioCreative organizing committee

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