Call: Literature Data Mining for Biology

Thierry Hamon thierry.hamon at
Fri Apr 27 09:43:36 UTC 2001

Date: Thu, 26 Apr 2001 16:00:18 -0400
From: Pamela J Davis <pjdavis at>
Message-Id: <3AE87E52.7FE7275F at>


			A call for papers in
                    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
   * 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.


Session co-chairs

   * Lynette Hirschman, MITRE
	lynette at
   * Jong C. Park, KAIST
	park at
   * Junichi Tsujii, University of Tokyo
	tsujii at
   * Limsoon Wong, KRDL
	limsoon at
   * Cathy Wu, National Biomedical Research Foundation & Georgetown
	wuc at


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

All papers must be submitted to russ.altman at 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.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 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.

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