BioTM-2010: Advances in Bio Text Mining / Call for Abstracts

Workshop BioTM-2010: Advances in Bio Text Mining

May 10-11, 2010, Ghent, Belgium


Abstracts are invited for the two-day workshop to be held in Ghent on
the 10th and 11th of May 2010.
Participants are encouraged to submit an extended abstract to the
workshop. Authors of selected abstracts will present their work in a
five minute bullet talk and their posters will be presented in a poster
session. Submitted abstracts will be reviewed by the organising committee.

The best abstracts will be published in an abstract supplement of BMC
Bioinformatics (
Submission deadline: April 1, 2010.


The program of the workshop includes:
– an extensive tutorial on Bio Text Mining by Martin Krallinger
– invited talks by leading scientists in the field: Sampo Pyysalo, Kevin
Cohen and Filip Ginter
– invited talks by experienced scientists from industry: Jean-Marc
Neefs, Luc Dehaspe and Maté Ongenaert


Text mining has become indispensible in many biological and biomedical
sciences. Having to keep up with an increasing number of publications,
text mining techniques enable retrieval and analysis of large amounts of
documents in a fully automated fashion. They allow for extraction of
facts described in the literature that have not yet been recorded in
databases, thus providing a necessary tool to obtain a complete overview
of all available knowledge.

Recently, the application of text mining and natural language processing
techniques to the biological and medical sciences has recieved
increasing interest. In addition to many new workshops and conferences
arising in this domain, recently also a number of community-wide tasks
were conducted to benchmark text mining techniques on specific
challenges (e.g. BioCreative, BioNLP Shared Task, …).

By discussing the latest developments and potentially new applications
in text mining amongst scientists in both academia and industry, this
workshop aims to provide a broad view on text mining tools in biology
and biomedicine. We are reaching out to a broad public, including
researchers with an interest in text mining but with little or no
experience in this domain. To this end, the workshop will start with an
extensive tutorial on text mining in the bio-sciences, providing
sufficient background knowledge for novices.

Next, a number of keynote talks will be given by leading scientists,
presenting the latest advances in the field. Furthermore, participants
are highly encouraged to submit an abstract describing their own work.
They will be given the opportunity to present this work in 5min flash
presentations, as well as to present a poster during the coffee and
lunch breaks.

Finally, we plan on having a round-table discussion about the broader
applicability of text-mining tools in the biological sciences, trying to
bridge the gap between theoretical algorithms and experimental work.



Submissions should present work related to any aspect of biomedical text
mining and bioinformatics. Additionally, we strongly encourage
submissions that describe shortcomings of current existing techniques,
tools, or resources, in order to detect problematic issues and work
towards their improvement.


An abstract of maximum 400 words with at most 1 table or figure should
be submitted to the following e-mail address in pdf format:
biotm2010 at gmail dot com
Detailed formatting instructions can be found at
Submission is blind.



1 April 2010 Submission deadline
15 April 2010 Notification of acceptance
30 April 2010 Camera-ready abstracts due
10-11 May 2010 Workshop in Ghent



Yvan Saeys
Thomas Abeel
Sofie Van Landeghem

Bioinformatics and Evolutionary Genomics group
VIB Department of Plant Systems Biology
Ghent University, Belgium

Walter Daelemans
Roser Morante
Vincent Van Asch

CLiPS – Text Mining Group
Faculty of Arts
University of Antwerp, Belgium