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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 now?

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
  • Representation and discovery of biomedical domain knowledge

All accepted papers will be published in the conference proceedings that will be available online. We are also currently discussing further publication of selected papers 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.

Submissions should follow the ACL two-column style, with a limit of eight (8) pages for full papers and four (4) pages for short papers, including references. Manuscripts will be submitted electronically as PDF files. Reviewing will be double-blind, and submissions should therefore NOT contain author names or other obviously identifying information. Detailed instructions and style files can be found on the conference webpage.

Important dates

May 1, 2008 Tutorial proposal submission deadline
June 18, 2008 Paper submission deadline (extended)
July 15, 2008 Notification of acceptance
August 7, 2008 Camera-ready deadline
September 1-3, 2008 Conference

Invited speakers

  • Alfonso Valencia (CNIO, Madrid, Spain)
  • Pierre Zweigenbaum (LIMSI-CNRS, Orsay, France)


Symposium co-chairs

  • Dietrich Rebholz-Schuhmann (EMBL-EBI, Hinxton, UK)
  • Tapio Salakoski (TUCS, Turku, 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 Library of Medicine, USA)
  • Anita Burgun (University of Rennes, France)
  • Kevin Cohen (University of Colorado, USA)
  • Nigel Collier (National Institute of Informatics, Japan)
  • Juliane Fluck (Fraunhofer SCAI, 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 (Link√∂ping 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)
  • 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)
  • Anna Santanen (University of Turku, Finland)