Appel: Translating Biology: Text Mining Tools That Work, PSB session

Thierry Hamon thierry.hamon at LIPN.UNIV-PARIS13.FR
Fri Jun 8 15:21:53 UTC 2007

Date: Wed, 06 Jun 2007 20:09:59 +0100
From: Ruslan Mitkov <R.Mitkov at>
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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

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

Session chairs:

Lynette Hirschman, The MITRE Corporation

Kevin Bretonnel Cohen (Contact person)
University of Colorado School of Medicine
kevin.cohen at

Philip Bourne
University of California San Diego

Hong Yu
University of Wisconsin at Milwaukee

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