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SMBM 2008 : Third International Symposium on Semantic Mining in Biomedicine


Conference Series : Semantic Mining in Biomedicine
When Sep 1, 2008 - Sep 3, 2008
Where Turku, Finland
Submission Deadline Jun 1, 2008
Notification Due Jul 17, 2008
Categories    NLP

Call For Papers


Third International Symposium on Semantic Mining in Biomedicine
(SMBM 2008)

September 1-3 2008, Turku, Finland

The biomedical research community eagerly awaits the full
integration of text, biological databases, ontologies and
terminological resources. However, many challenges have yet to be
met to achieve this ambitious goal. Significant advances have been
made and many working systems (e.g. for entity recognition and
simple relation extraction) have been proposed. Where do we stand

The third International Symposium on Semantic Mining in Biomedicine
(SMBM 2008), organized by Turku Centre for Computer Science (TUCS),
aims to bring together different communities: researchers from text
and data mining in biomedicine, medical-, bio- and
cheminformaticians, and researchers from biomedical ontology design
and engineering. This is the follow-up event of SMBM 2005
(EMBL-EBI, U.K.) and SMBM 2006 (Friedrich-Schiller University of
Jena, Germany).

We are inviting papers from a full range of topics (see below),
emphasizing in particular work on methods deployed in a
production-like research environment, the integration of text with
domain resources such as micro-array data and ontological resources
such as GO, UMLS etc. as well as work on the challenges and novel
approaches in biomedical information extraction going beyond the
detection of pairs of related entities.

Topics of interest include (but are not limited to):

* Text mining, information extraction, and information retrieval
* Terminology and ontology development for biomedical information systems
* Evaluation techniques and standards for text mining solutions
* Integration of text and data mining in the biomedical domain
* Annotation schemes for biomedical corpora
* Text mining for resource building, e.g. ontologies

All accepted papers will be published in the conference proceedings
that will be available online. Additionally, we aim to have
selected papers published in a biomedical journal similarly to SMBM
2005 (J. of Bioinformatics) and SMBM 2006 (BMC Bioinformatics
Supplement). We invite both full and short papers, where full
papers will be given an oral presentation and short papers
presented as posters. Detailed instructions to authors will be
published soon on the conference webpage.

Important dates

May 1, 2008 Tutorial proposal submission deadline
June 1, 2008 Paper submission deadline
July 15, 2008 Notification of acceptance
August 7, 2008 Camera-ready deadline
September 1-3, 2008 Conference

Invited speakers

* Alfonso Valencia (CNIO, Spain)
* Pierre Zweigenbaum (STIM, France)


Symposium co-chairs

* Dietrich Rebholz-Schuhmann (EMBL-EBI, UK)
* Tapio Salakoski (TUCS, Finland)

Local organizing chair

* Sampo Pyysalo (University of Turku and TUCS, Finland)

Programme committee

* Sophia Ananiadou (University of Manchester and NaCTeM, UK)
* Christopher J. O. Baker (I2R, Singapore)
* Olivier Bodenreider (National Network of Libraries of Medicine, USA)
* Anita Burgun (University of Rennes, France)
* Kevin Cohen (University of Colorado, USA)
* Nigel Collier (National Institute of Informatics, Japan)
* Juliane Fluck (SCAI, Fraunhofer, Germany)
* Carol Friedman (University of Columbia, USA)
* Filip Ginter (University of Turku, Finland)
* Udo Hahn (University of Jena, Germany)
* Lynette Hirschman (MITRE, USA)
* Su Jian (I2R, Singapore)
* Jin-Dong Kim (University of Tokyo, Japan)
* Satoshi Kobayashi (University of Electro-Communications, Japan)
* Michael Krauthammer (Yale University School of Medicine, USA)
* Patrick Lambrix (Linköping University, Sweden)
* Adeline Nazarenko (Universite Paris-Nord, France)
* See-Kiong Ng (NTU and I2R, Singapore)
* Jong C. Park (KAIST, South Korea)
* Martin Romacker (Novartis Pharma AG, Switzerland)
* Jasmin Saric (Boehringer Ingelheim Pharma GmbH, Germany)
* Gerold Schneider (University of Zurich, Switzerland)
* Stefan Schulz (Freiburg University Hospital, Germany)
* Hagit Shatkay (Queen's University, Canada)
* Jun'ichi Tsujii (University of Tokyo, Japan and University of
Manchester, UK)
* Alfonso Valencia (CNIO, Spain)
* Simo Vihjanen (Lingsoft, Finland)
* Limsoon Wong (National University of Singapore)

Local organizers

* Filip Ginter (University of Turku, Finland)
* Hanna Suominen (University of Turku and TUCS, Finland)

Further information

Symposium organizers' contact address


Symposium web page



We are soliciting proposals for tutorials that cover any of the topics
of interest of the conference, such as text mining methods and tools,
ontologies, terminologies and corpora, or integration of text and data
mining. Tutorials will span half a day on Monday, September 1st.
Proposals should list the goal, content and structure of the tutorial.

The deadline for SMBM 2008 tutorial submission is May 1, 2008.
Notification of acceptance will be given by June 1, 2008. Proposals
should be submitted electronically in PDF format to the email address

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