A Pacific Symposium on Biocomputing Session
The Big
Motivation|Submission requirements|Session chairs|Submission information
Biomedical science is now an information-intensive field of study, with high-throughput experimental techniques generating large amounts of data, and bioinformatics providing tools for managing and making sense of that data. However, the information generated and used in biomedical science must be accessible both to computers and to people. This requires constant translation between human-readable forms, such as text and figures, to computer-readable forms, such as biological databases and ontologies. In a recent PLoS Computational Biology editorial, Philip Bourne posed the following question: Will a biological database be different from a biological journal? If we had text mining tools that worked, then the translation from text to database (and back) would blur these lines. Such tools would enable the seamless incorporation of semantic information extracted from text with databases and with analytical tools, as just one of many sources of information in addressing complex biological problems.
From the many publications in the area, we know that
performance has reached reasonable levels on a number of basic text mining
tasks, such as indexing and the identification of biomedical entities. We now
need to ask a new set of questions: Do these tools work? Can they be adapted to
new applications? Are they cost-effective in real applications? Who uses these
tools, and how? Can these tools be maintained over time? The answers to these
questions are critical to understanding the apparent gap between the number of
publications on biomedical text mining and the
number of deployed text mining applications. The answers to these
questions are also essential to providing the bioinformatics community with the
text mining tools that they are asking for. We categorize these questions into
four attributes: utility, usability, portability, and robustness.
The proposed session will focus on papers that explore these issues, including
questions such as:
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
Paper submissions due:
Notification of paper acceptance:
Final paper deadline: September 24, 2007 midnight PT
Abstract deadline: November 9, 2007
Meeting:
All papers must be submitted to psb-submit
@ helix.stanford.edu and kevin.cohen @ gmail.com in electronic format with PSB in the subject line. The file formats we accept
are: postscript (*.ps) and Adobe Acrobat (*.pdf). Attached files should be
named with the last name of the first author (e.g. altman.ps or altman.pdf).
Hardcopy submissions or unprocessed
Each paper must be accompanied by a cover letter. The cover letter must
state the following:
Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. 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.
Contact Russ Altman (psb-submit @ helix.stanford.edu) for additional information about paper submission requirements.