Call for Papers
Text
and Data Mining for Biomedical Discovery
Pacific Symposium on Biocomputing
January 3-7, 2014
Fairmont Orchid, Big Island
Hawaii, U.S.A.
The
biggest challenge for text and data mining in biomedical informatics is to
impact the discovery process, enabling scientists to generate novel hypothesis
to address the most crucial questions for
understanding the molecular basis of human diseases.
However, formulation of a flexible and general approach for integrating
heterogeneous data and knowledge sources for discovery is elusive and highly
dependent upon the specific underlying scientific question. Thus, the true
impact of text and data mining is only realized if it goes beyond the methods
for extraction or pattern recognition, and into enabling understanding of the
molecular underpinnings of biological processes.
This
session will bring together researchers with a strong background in either text
or data mining who are collaborating with bench scientists for the deployment
of integrative approaches in translational bioinformatics. It serves as a
unique forum to discuss novel approaches to text and data mining methods that
respond to specific scientific questions, enabling predictions that integrate a
variety of data sources and can potentially impact scientific discovery.
We seek contributions where the data or
text mining aspects are so tightly coupled to their corresponding biological/pharmacological/genomic
aspects for their significance, that neither aspect of the work can be
de-emphasized or understood without the other; work where the biology
significantly enhances and informs the text and data mining methods, and vice
versa.
Some examples of topics of interest to
this session include novel approaches that integrate empirical data with
knowledge extracted from the literature, curated databases, relevant ontologies
and other sources to perform discovery-related tasks such as:
- Gene prioritization
- Binding site prediction
- Gene/protein function
prediction,
- Prediction of associations
(protein-protein, gene-drug, gene-disease, drug-drug, and others)
- Pathway generation or
validation
for translational applications
such as pharmacogenomics and personalized medicine (genome-phenome
validation, or disease detection, diagnosis and prognosis). Submissions should clearly state the
translational value of their contribution.
Session Organizers
Chair:
Graciela H. González
Arizona State University
Co-Chairs:
Kevin Bretonnel
Cohen
U.
Colorado School of Medicine
Maricel G. Kann
University of Maryland,
Baltimore County
Casey Greene
Dartmouth
Robert Leaman
National
Center for Biotechnology Information (NLM/NCBI)
Nigam Shah
Stanford University
Jieping Ye
Arizona State University
Submission
Information
Please note that the submitted papers are reviewed and accepted on a competitive basis. At least three reviewers will be assigned to each submitted manuscript.
Important Dates
Paper
submissions due: July 31, 2013
Notification
of paper acceptance: September 9, 2013
Final
paper deadline: October 1, 2013 at 11:59pm PT
Registration
opens: August 1, 2013 at noon PT
Travel award applications
PSB has been able to offer travel
support to many attendees in the past. However, please note that no one is
guaranteed travel support.
Available:
August 1, 2013 at noon PT
Deadline:
October 7, 2013 at noon PT
Decisions will be announced in
mid-October.
For details, please see http://psb.stanford.edu/keydates.html
Paper Format
Please see the PSB paper format template and
instructions at http://psb.stanford.edu/psb-online/psb-submit.
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 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 http://psb.stanford.edu/psb-online/psb-submit/. If figures cannot 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.