Title:    Bioinformatics and NLP Issues 

Speakers: Professor Toshihisa Takagi
          Human Genome Center
          Institute of Medical Science, University of Tokyo
          4-6-1 Shirokane-dai Minato-ku Tokyo 108-8639, Japan
          Phone:+81-3-5449-5611
          email: takagi@ims.u-tokyo.ac.jp

          Dr. Ken-ichiro Fukuda
          Computational Biology Research Center (CBRC),
          National Institute of
          Advanced Industrial Science and Technology (AIST)
          2-41-6 Aomi, Koutou-ku, Tokyo  135-0064  JAPAN
          Phone: +81-3-3599-8049
          email: fukuda-cbrc@aist.go.jp

          Dr. Takako Takai-Igarashi
          Human Genome Center
          Institute of Medical Science, University of Tokyo
          4-6-1 Shirokane-dai Minato-ku Tokyo 108-8639, Japan
          Phone:+81-3-5449-5614
          email: takako@ims.u-tokyo.ac.jp

Summary:  Biology is a ``knowledge-based'', rather than an ``axiom-based''
          discipline and thus the availability of pre-existing knowledge is
          vital. Supported by the conviction that scientific articles encode
          knowledge not appearing in biological databases, a research area
          applying NLP techniques to biological text has recently blossomed.
          The central subject is focused on Information Extraction, while other
          subjects include methods that try to improve clustering results of
          biological data by utilizing document similarities.

            The aim of this tutorial is to outline and understand the
          fundamental nature of biological knowledge in bioinformatics. The
          first part will describe the history of bioinformatics from the
          viewpoint of database development. Then we will provide a survey of
          researches in bioinformatics that utilize biological texts. The second
          part will discuss the diversity and richness of knowledge described in
          scientific articles by focusing on signal transduction pathway domain,
          an area that tries to describe the mechanisms of various life
          phenomena in terms of interactions of proteins and other biomolecules.

Course Outline:

     PART 1:
          (1) History of genome science; 
          (2) Significance of knowledge buried in biological texts and
              its utilization; 
          (3) Survey of prominent researches in the past and the current
              situation of this field; 
          (4) Open challenges in NLP for bioinformatics. 

     PART 2:
          (5) Biological primer for genome science; 
          (6) Examples of biological information described in texts; 
          (7) The use of ontology in biology; 
          (8) Introduction of our ontology for signal transduction pathways; 
          (9) Lastly we would like to discuss with participants the future
              of this research field

Bio:     Professor Toshihisa Takagi

         Research interests: knowledge representation and simulation of
             living system, genome ontology.

         Areas of expertise: bioinformatics, database.

         ------------

         Dr. Ken-ichiro Fukuda 

         Research interests: Development and application of bioinformatics
             methods for problems in describing living systems. Application
             of artificial intelligence and data mining techniques to the
             representation and extraction of higher-level biological
             knowledge.

         Areas of expertise: knowledge engineering, ontologies, bioinformatics.

         ------------

         Dr. Takako Takai-Igarashi

         Research interests: Analyze fundamental mechanisms of living system
             from computational approaches.   

         Areas of expertise: knowledge representation, bioinformatics.