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-- Proceedings now available online on Springer Verlag --

International Workshop on

Knowledge Systems in Bioinformatics (KSinBIT'06)

Oct 29, 2006
Montpellier, France

In conjunction with OnTheMove Federated Conferences (OTM'06)

Proceedings will be published by Springer LNCS

Call for papers

The impact of the upcoming Internet on scientific research worldwide was enormous, not the least in biomedical research. Especially the Human Genome Project was the inspiration for many biological databases publicly available via the Internet. As of now, conducting biomedical research without the Internet is nearly impossible. The information needed for analysis and interpretation of experimental results is usually scattered over a multitude of heterogeneous data sources: sequence databases (Genbank, Swiss-Prot/TrEMBL), protein resources (iProClass (PIR), PDB, InterPro), gene expression data repositories (GEO, ArrayExpress), literature databases (PubMed, Web of Science), functional annotation databases (GO, Kegg), etc. Many researchers depend on the Internet as the most important source of biomedical information. As the amount of available data increases at a rate never seen before, researchers are now faced with the problem of finding the information they need, in a format they can work with.

Several initiatives exist that try to integrate multiple data sources (SRS, Ensembl, Entrez Gene) or facilitate complex bioinformatics queries (Biozon) and analyses (BioMOBY, myGrid). However, the integration is not always in tune with the user’s requirements for information. This is were emerging Internet technologies can help. Semantic web technologies, like ontologies, will enable fast, context-sensitive retrieval of biological data. Web services will allow extensive automatization of complex bioinformatics tasks and drive the standardization process. Grid computing will transform the Internet in a gigantic instrument for solving the mystery of life. Yet, that is the future.

The aim of this workshop is to bring together researchers and practitioners to exchange ideas with respect to knowledge systems in bioinformatics that make extensive use of medical and biological semantics and ontologies, web services technologies, and/or distributed databasing and computing to tackle the issues mentioned above. We invite all researchers working in this cross-section between information technology and biomedical research to contribute.


Topics of interest may include one or more of the following (but are not limited to) themes;

  • Medical and biological ontologies and taxonomies
  • Biomedical data management
  • Data source integration
  • Conceptual integration through visualization
  • Semantic web applications in bioinformatics
  • Bioinformatics web services
  • Ontology driven mediation
  • Automated functional annotation using ontologies
  • Automated knowledge discovery
  • In silico hypthesis testing
  • Middleware for in silico experimentation
  • Workflow management in bioinformatics


Papers submitted to KSinBIT 2006 must not have been accepted for publication elsewhere or be under review for another workshop or conference. All submitted papers will be carefully evaluated based on originality, significance, technical soundness, and clarity of expression. All submissions must be in English. Submissions should be in PDF format and must not exceed 10 pages in the final camera-ready format. Authors instructions can be found at:

The paper submission site is located at:

Failure to commit to presentation at the conference automatically excludes a paper from the proceedings.


  Abstract Submission Deadline   June 15, 2008 Extended until July 7, 2008
Paper Submission Deadline June 30, 2008 Extended until July 7, 2008
Acceptance Notification August 15, 2008
Camera Ready Due August 25, 2008
Registration Due August 25, 2008
OTM Conferences November 9 - 14, 2008


Program Chairs

  • Maja Hadzic
    Centre for Extended Enterprise and Business Intelligence
    Curtin University of Technology, Perth, Australia
  • Bart De Moor
    Katholieke Universiteit Leuven, Belgium
  • Yves Moreau
    Katholieke Universiteit Leuven, Belgium
  • Arek Kasprzyk
    European Bioinformatics Institute
    Hinxton, Cambridge, United Kingdom

Program Committee Members

  • Robert Meersman - STARLab, VUB
  • Werner Ceusters - Ontology Research Group (ORG)
  • Georges De Moor - Ghent University (RUG)
  • Elizabeth Chang - Curtin University of Technology
  • Peter Dawyndt - Biometrics and Process Control (Ghent University)
  • Jan Van den Bussche - University of Hasselt
  • Antoon Goderis - University of Manchester
  • Paolo Romano - National Cancer Research Institute (IST)
  • Marie-Dominique Devignes - Centre National de la Recherche Scientifique, LORIA (Nancy), France
  • Bert Coessens - ESAT - SCD, Katholieke Universiteit Leuven
  • Mark Wilkinson - University of British Columbia
  • Katy Wolstencroft - University of Manchester
  • Peter Li - University of Manchester
  • Robert Stevens - University of Manchester
  • Carole Goble - University of Manchester
  • Phillip Lord - University of Newcastle-Upon-Tyne, UK
  • Chris Wroe - British Telecom
  • Michael Bada - University of Colorado and Health Sciences Center
  • Ilkay Altintas - San Diego Supercomputer Center, UCSD, USA
  • Stephen Potter - The University of Edinburgh
  • Vasa Curcin - Imperial College London
  • Armin Haller - National University of Ireland
  • Eyal Oren - National University of Ireland
  • M. Scott Marshall - University of Amsterdam
  • Marco Roos - University of Amsterdam
  • Iwei Yeh - Stanford University

This is a joint workshop organised by Vrije Universiteit Brussel (VUB, Belgium) and Katholieke Universiteit Leuven (KUL, Belgium), and co-organised with BioScope-IT, the Flemish Bioinformatics Network (Belgium).