A call for paper in

Natural Language Processing for Biology:
Term extraction, Information retrieval, Information extraction,
and Corpus Annotation

A special session within the
Pacific Symposium on Biocomputing 2001
January 3-7, 2001
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, information extraction, information retrieval, and bioinformatics to present and exchange ideas and results on this exciting emerging subject. We welcome technical papers covering algorithms, techniques, and applications in the following areas of interest:

• Automatic term extraction from biology texts using NLP techniques
• Information extraction from sources such as MEDLINE abstracts
• Information retrieval from scientific journals and existing databases using NLP
• Biology corpora annotations

• use natural language means to extract terms, gene names, protein names, biological materials and methods, protein interactions, functions, etc.
• demonstrate novel natural language-based applications in biology

Session co-chairs

• Junichi Tsujii, University of Tokyo, Japan
  tsujii@is.s.u-tokyo.ac.jp
• Limsoon Wong, Kent Ridge Digital Labs, Singapore
  limsoon@krdl.org.sg

Submission information

All papers must be submitted to russ.altman@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.