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BioLINK SIG 2013: Roles for text mining in biomedical knowledge discovery and translational medicine-Call for Papers

Date: 12th April 2013

Location: Berlin, Germany

CALL FOR PAPERS, BioLINK SIG 2013: Roles for text mining in biomedical knowledge discovery and translational medicine

Meeting of the Special Interest Group on Linking Literature, Information and Knowledge for Biology
at ISMB/ECCB 2013  
Berlin, Germany
July 19-23, 2013

Important dates:

April 12th, 2013    Short and Full paper Submissions Due
May 17th, 2013    Notifications for short and full papers
May 20th, 2013    Poster abstracts due
May 24th, 2013    Final paper versions due
July 20th, 2013    BioLINK SIG meeting at ISMB

We solicit submissions from researchers working on all aspects of mining text in the biological, medical and clinical domains, with a specific emphasis on the use of text mining in the translational medicine or precision medicine contexts.

With the increasing availability of text data related to biology and medicine in the scientific literature, database annotations, the electronic health record, clinical trials data, and health information online, exciting opportunities arise to provide access to pertinent biomedical information and to advance biomedical knowledge. An evolving research direction is the integration of information from diverse data sources, including textual data, to support deeper understanding of biological systems, the genomic basis of disease, and genotype-phenotype relationships.

This year we aim to focus the BioLINK SIG Workshop on text-based applications which link between biological and clinical information. We will build on the topic of the well-attended previous special session on data integration, but shift the focus towards the use of text mining in applications that aim to further biological or medical understanding. As such, we encourage submission of papers on the following topics:

Text mining methods development

   • integration of clinical text with the published literature
   • information extraction of biological and clinical information, with an emphasis on
       • recognition of phenotype descriptions in text
       • extraction of biological pathways or networks
   • mining of social media for biomedical information

We strongly encourage papers which describe applications of text mining for:

   • precision medicine
   • personal genomics
   • translational medicine
   • computational drug discovery or repositioning
   • high-throughput biological data interpretation
   • genetic variant interpretation

We will accept three types of submissions of new, previously unpublished research. Poster abstracts will be reviewed for relevance to the topics of the workshop; short and long papers will be peer-reviewed. Accepted full papers will be allocated a longer time slot than accepted short papers, with the specific allocations to be determined.

   • Full papers (maximum 7 pages, 2-column format, including references)
   • Short papers (maximum 4 pages, 2-column format, including references)
   • Poster abstracts (maximum 1 page, 2-column format, including references)

Please use the EasyChair website to upload your paper manuscript by 11:59pm on April 12, in the time zone of your choice:

Poster abstracts can be submitted to the same site, by 11:59pm on May 13, in the time zone of your choice.

Organizing Committee

Christian Blaschke, Spanish Institute of Bioinformatics
Lynette Hirschman, MITRE Corporation
Hagit Shatkay, Dept. of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware
Alfonso Valencia, Spanish National Cancer Research Centre
Karin Verspoor, National Information and Communication Technology Australia (NICTA)

Program Committee

Sophia Ananiadou, University of Manchester and NACTEM
Alan Aronson, US National Library of Medicine
Kevin Bretonnel Cohen, University of Colorado School of Medicine
Anna Divoli, Pingar Research
Larry Hunter, University of Colorado School of Medicine
Martin Krallinger, Spanish National Cancer Research Centre
Zhiyong Lu, US National Library of Medicine
Dietrich Rebholz-Schuhmann, University of Zurich and the European Bioinformatics Institute
Phoebe Roberts, Pfizer
Luis Rocha, Indiana University
Jun'ichi Tsujii, Microsoft Research Asia
John Wilbur, US National Library of Medicine


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