ISMB BioLINK 2009

Call for Papers

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The Ninth Annual Meeting of the ISMB BioLINK Special Interest Group: Text Mining, Image Analysis, and the future of Scientific Publishing

In association with ISMB 2009, Stockholm, Sweden. The BioLINK SIG will take place on Sunday, June 28 – Monday June 29, 2009 See http://www.cs.queensu.ca/biolink09 for details and updates.

New this year: The SIG will go beyond text to take into account the analysis of images and figures in scientific publications, because of their critical information content. Furthermore, we will include a session about the future of scientific publishing, and the impact of information extraction methods (be they based on text or on images) on producers and consumers of scientific information.

With the increasing availability of publications and text related to biology, including Medline abstracts and full-text journal articles, the field of biomedical text mining has been rapidly maturing. It is concerned with using techniques from natural language processing, information extraction and information retrieval to automate knowledge discovery from biomedical text. As much of the published material includes images, which are of utmost importance for both scientists and database curators, the ability to automatically and effectively mine image data is becoming increasingly critical – and draws much interest. Thus the SIG this year will look at both aspects of published knowledge – text and images.

As in previous years, the SIG will be interdisciplinary in nature, and will bring together researchers developing text and image mining techniques, with scientists from bioinformatics and biology who are potential end users of this technology.

We solicit submissions from researchers working on all aspects of mining text and image data in the scientific literature as they apply to bioinformatics and bio-medicine. Suggested topics include (but are not limited to):

to end users. mining in the biomedical domain. bioinformatics workflows.
 * New applications for text mining: bringing together end users and developers.
 * Image analysis within documents/papers/publications.
 * Integration of text and image data to address specific information needs.
 * Emerging text and image mining tools, and how to make these tools available
 * New methods, measures and corpora for testing and evaluating literature
 * Examples of text and image mining used to assist in database curation
 * Incorporation of text-mining derived data into larger biological and

The SIG provides an informal forum for presentation and discussion of current research in the field. The program will include presentations of short papers, posters and invited talks.

We are inviting submission in two categories: 1) short papers (up to 4 pages) 2) poster abstracts (up to 300 words). Submissions, in PDF or MS word, should be sent, by the dates specified below, to: biolink09@cs.queensu.ca

Authors should indicate the category for which their paper is to be considered (short paper or poster in the subject line), and whether they would like their work to be considered for an oral presentation. All accepted papers will be included in the ISMB SIG notes. We are also considering the possibility of having selected SIG papers revised and published as a special issue of a journal in the area of bioinformatics.

Important Dates: April 5: Short papers (up to 4 pages) due April 15: Poster Abstracts (up 350 words) due May 5: Notification to authors May 15: Final version due

To register for BioLINK SIG, use the ISMB'09 registration form (http://www.iscb.org/ismbeccb2009/).

Program Chairs:

Christian Blaschke, Bioalma, Spain Hagit Shatkay, School of Computing, Queen's University, Canada Lynette Hirschman, MITRE Corp., USA Scott Markel, Accelrys' R&D group, USA Robert F. Murphy, Carnegie Mellon University,Pittsburgh, USA Alfonso Valencia, Spanish National Cancer Research Centre, Spain

Contact and submission email: biolink09@cs.queensu.ca	 This CfP was obtained from WikiCFP