Appel: NLP for Biology

Philippe Blache pb at
Mon Jul 5 07:08:03 UTC 1999

From: tatsu at

With Apologies for possible multiple deliveries of this message.


                    A call for paper in


                A special session within the
          Pacific Symposium on Biocomputing 2000
                    January 5-9, 2000
                    Honolulu, Hawaii


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. Such
information is important for many types of analysis, such as
classification of proteins into functional groups, discovery of new
functional relationships, maintaining information of material and
methods, increasing the precision and relevance of hits returned by
information retrieval systems, and so on.

However, information in free-text form or in comment fields is very
difficult for use by automated system. For example, annotation of
biological function of different proteins is a time-consuming process
currently performed by human experts because genome analysis tools
encounter great difficulty in performing this task. The ability to extract
information directly from MEDLINE abstracts and other sources can
directly help in such a task.

This special session provides an international forum for researchers
from the fields of natural language processing (NLP), information
extraction, and bioinformatics to present and exchange ideas and
results on this exciting emerging subject. We welcome technical papers
covering algorithms, techniques, and applications. We particularly
encourage submissions describing systems that

 - use NLP means to extract keywords, gene names, protein names,
   biological materials and methods, protein interactions, functions,

 - demonstrate novel natural language-based applications in biology

Also, NLP technologies sometimes contribute to analyzing genomic
sequences. Their grammar-class varies from regular to context
sensitive (or even higher) according to how precise we define their
structure. Which classes and parsing technologies are appropriate for
searching functional sites or genes is still an open question. Thus we
also welcome original papers describing how NLP techniques have
brought break-throughs in genomic sequence analysis.

Session co-chairs

 - Tatsuhiko Tsunoda, University of Tokyo, Japan
 - Limsoon Wong, Kent Ridge Digital Labs, Singapore

Submission information:

  Submissions are due     12 July 1999
  Decisions are announced 27 August 1999
  Camera ready copy due   22 September 1999

All papers must be submitted to 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.


Tatsuhiko TSUNODA, Ph.D.
Human Genome Center,
Institute of Medical Science,
University of Tokyo
4-6-1 Shirokanedai, Minato-ku,
Tokyo 108-8639, Japan
TEL: +81-3-5449-5614
FAX: +81-3-5449-5434
E-mail: tatsu at

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