[Corpora-List] Translating Biology: Text Mining Tools That Work. A Pacific Symposium on Biocomputing Session

[Ruslan Mitkov]

Please post. Thank you.

Ruslan Mitkov

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Call For Papers

Translating Biology: Text Mining Tools That Work

A Pacific Symposium on Biocomputing Session

January 4-8, 2008
The Big Island, Hawai'i

<http://psb.stanford.edu/cfp-nlp.html>http://psb.stanford.edu/cfp-nlp.html

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 for 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 session will focus on papers that explore these issues, including
questions such as:


What is the actual utility of text mining in the work flows of the various
communities of potential users­model organism database curators, bedside
clinicians, biologists utilizing high-throughput 
experimental assays, hospital billing departments?

How usable are biomedical text mining applications? How does the application
fit into the workflow of a complex bioinformatics pipeline? What kind of
training does a bioscientist require to be able to use an application?

Is it possible to build portable text mining systems? Can systems be adapted
to specific domains and specific tasks without the assistance of an
experienced language processing specialist?

How robust and reliable are biomedical text mining applications? What are the
best ways to assess robustness and reliability? Are the standard evaluation
paradigms of the natural language processing world­intrinsic evaluation
against a gold standard, post-hoc judging of outputs by trained judges,
extrinsic evaluation in the context of some other task­the best evaluation
paradigms for biomedical text mining, or even sufficient evaluation paradigms?

Submission information

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 noon,
November 9, 2007 to present their work in the poster sessions.

Important dates

Paper submissions due: July 16, 2007
Notification of paper acceptance: September 5, 2007
Final paper deadline: September 24, 2007 midnight PT
Abstract deadline: November 9, 2007
Meeting: January 4-8, 2008

For full submission information, including style sheets and
all requirements, please see the session web site at
<http://psb.stanford.edu/cfp-nlp.html>http://psb.stanford.edu/cfp-nlp.html.

Session chairs:

Lynette Hirschman, The MITRE Corporation

Kevin Bretonnel Cohen (Contact person)
University of Colorado School of Medicine
<mailto:kevin.cohen at gmail.com>kevin.cohen at gmail.com

Philip Bourne
University of California San Diego

Hong Yu
University of Wisconsin at Milwaukee