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Olivier Bodenreider olivier at
Tue Jul 1 10:34:49 PDT 2003


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					Second Call for Papers and Posters

                           Biomedical Ontologies

               at the Pacific Symposium on Biocomputing 2004
                            January 6-10, 2004
                 The Fairmont Orchid, Big Island of Hawaii


As we celebrate the 50th anniversary of the description of the structure of
DNA, biology is evolving from a science of organisms and molecules to a
science of information. In modern biology, massive amounts of data are
produced resulting, for example, from sequencing the genome of many
organisms and studying gene expression under various conditions. In turn,
there has been a shift from hypothesis-driven experiments to data-driven

Ontologies provide a conceptualization of a domain that can be shared among
diverse groups of researchers and health care professionals and used
computationally for multiple purposes. Biologic knowledge is evolving so
rapidly that it is difficult for most scientists to assimilate and
integrate the new information with their existing knowledge. Promoting the
creation and use of ontologies for the field and linking to other
ontologies in related domains holds the promise of assisting those working
in biomedical disciplines and thus making more rapid scientific progress.

This session would welcome papers that discuss:

* Biomedical ontology creation and use
* Reasoning about the biomedical domain based on ontological knowledge
* Use and development of ontologies to support natural language processing
* Ontologies in support of knowledge discovery
* Intelligent agent technologies and associated ontologies
* Scalability and versioning of biomedical ontologies
* Linking and aligning multiple ontologies
* Use of ontologies to bridge heterogeneous information resources (e.g., to
  connect genotype to gene expression and ultimately to clinical medicine,
  drug discoveries, etc.)
* Advances in ontology languages and related technologies as applied to
  bioinformatics and biomedical problems
* Other research associated with bioinformatics and biomedical ontologies


                           Session co-chairs 

* Olivier Bodenreider (contact person)
  National Library of Medicine
  olivier at

* Joyce A. Mitchell
  University of Missouri, Columbia and National Library of Medicine
  MitchellJo at

* Alexa T. McCray
  National Library of Medicine
  mccray at


                           Submission information

Papers and Posters

The core of the conference consists of rigorously peer-reviewed full-length
papers reporting on original work. Accepted papers will be published in a
hard-bound archival proceedings, and the best of these will be presented
orally to the entire conference. Researchers wishing to present their
research without official publication are encouraged to submit a one page
abstract by November 1, 2003, and present their work in the poster

Important dates

* Paper submissions due:            July 14, 2003
* Notification of paper acceptance: September 8, 2003
* Final paper deadline:             September 22, 2003
* Abstract deadline:                November 1, 2003
* Meeting:                          January 6-10, 2004

Paper format

All papers must be submitted to russ.altman at in electronic
format. The file formats we accept are: 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

Contact Russ Altman (russ.altman at for additional information
about paper submission requirements.

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