Appel: Literature Data Mining for Biology

alexis nasr alexis.nasr at
Wed Jun 20 16:31:50 UTC 2001


                   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

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

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

(*.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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