Corpora: SECOND CALL FOR PAPERS--Pacific Symposium on Biocomputing 2002

[Pamela J Davis]

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                               SECOND CALL FOR PAPERS

                             Literature Data Mining for Biology

                                 A special session within the
                          Pacific Symposium on Biocomputing 2002
                                      January 3-7, 2002
                            Kauai Marriott Resort and Beach Club

 A large part of the information required for biology research can only
   be found in free-text form, as in MEDLINE abstracts, or in comment
  fields of relevant reports, as in GenBank feature table annotations.
   This information is important for many types of analysis, such as
  classification of proteins into functional groups, discovery of new
  functional relationships, maintenance of information on material and
 methods, increased  precision and relevance of hits returned by BLAST,
   extraction of protein interaction information, and so on. However,
information in free-text form or in comment fields is very difficult for

  automated systems to use. In addition, the extracted information may
  need further enrichment, for example, the inclusion of quantitative
                   information about the interaction.

   This session will investigate how natural language and data mining
techniques can provide and structure information relevant to biological
applications. The session solicits papers on techniques and applications

     of natural language processing to the extraction of biological
   information from free text, including literature abstracts (e.g.,
    MEDLINE), database annotations (e.g., GENBANK or PIR), and other
 relevant biology sources. It will emphasize the combination of natural
 language techniques with other biological information sources, such as
      database and sequence searches, to facilitate collection and
                   organization of information about
    particular genes, proteins, or pathways.  In particular, we are
                             interested in:

     * Novel ways of combining text data mining and more conventional
                   bioinformatics  search techniques;
     * Use of text data mining techniques for consistency checking and
       error detection in      annotation of existing data bases;
   * Biological problems where extraction of text-based information can
               provide quantitative    performance gains;
      * Evaluations of the utility of text data mining techniques and
                              components;
    * Extraction and organization of text-based information facilitated
              by ontologies and data  exchange standards;
     * Creation of structured resources (databases) through the use of
       text data mining and    information extraction techniques.


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                           Session co-chairs

                        * Lynette Hirschman, MITRE
                               lynette at mitre.org
                           * Jong C. Park, KAIST
                              park at nlp.kaist.ac.kr
                   * Junichi Tsujii, University of Tokyo
                           tsujii at is.s.u-tokyo.ac.jp
                           * Limsoon Wong, KRDL
                              limsoon at krdl.org.sg
      * Cathy Wu, National Biomedical Research Foundation & Georgetown
                               University
                            wuc at nbrf.georgetown.edu

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                         Submission information

                      Submissions are due 16 July 2001
                   Decisions are announced 31 August 2001
                  Camera ready copy due 24 September 2001
                    Poster abstracts due 5 November 2001
                Further information http://psb.stanford.edu

 All papers must be submitted to russ.altman at stanford.edu in electronic
format. The file formats we accept are: postscript (*.ps), adobe acrobat

 (*.pdf) and Microsoft Word documents (*.doc). Attached files should be
     named with the last name of the first author (e.g. altman.ps,
 altman.pdf, or altman.doc). Hardcopy submissions or unprocessed TEX or
              LATEX files will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter must
                          state the following:

              * The email address of the corresponding author
    * The specific PSB session that should review the paper or abstract
   * The submitted paper contains original, unpublished results, and is
             not currently   under consideration elsewhere.
          * All co-authors concur with the contents of the paper.

  Submitted papers are limited to twelve (12) pages in our publication
  format. Please format your paper according to instructions found at
ftp://ftp-smi.stanford.edu/pub/altman/psb. If figures can not be easily
 resized and placed precisely in the text, then it should be clear that
  with appropriate modifications, the total manuscript length would be
 within the page limit. Color pictures can be printed at the expense of
the authors. The fee is $500 per page of color pictures, payable at the
                    time of camera ready submission.