2nd CALL FOR PARTICIPATION: Fifth BioCreative Challenge workshop

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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.



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[Apologies for multiple postings]



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1. SCOPE

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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.





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2. TOPICS

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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



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3. DATES

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* Workshop date: 9-11th September 2015

* Poster abstract submission deadline: August 25th

* For track-related deadlines: check timelines:
http://www.biocreative.org/events/biocreative-v/CFP



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4. KEYNOTES

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* Prof. Ioannis Xenarios (Center for Integrative Genomics - University of
Lausanne; Vital-IT, SIB)

* Prof. Søren Brunak (University of Copenhagen; Technical University of
Denmark)





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5. CONFIRMED PANELITS

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Sophia Ananiadou, University of Manchester / NaCTeM

Jo McEntyre, 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







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6. BIOCREATIVE ORGANIZING COMMITTEE

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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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Martin Krallinger, Ph.D.
Structural Computational Biology Group
Structural Biology and BioComputing Programme
Spanish National Cancer Research Centre (CNIO)
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