2nd CALL FOR PARTICIPATION: Fifth BioCreative Challenge workshop
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.
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.
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
* Workshop date: 9-11th September 2015
* Poster abstract submission deadline: August 25th
* For track-related deadlines: http://www.biocreative.org/events/biocreative-v/CFP
* 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 PANELITS
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
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
For information:Martin Krallinger, Ph.D.
Structural Computational Biology Group
Structural Biology and BioComputing Programme
Spanish National Cancer Research Centre (CNIO)