Workshop on Natural Language Processing and Ontology Building in Biology

This Workshop is sponsored by
Genome Information Science Project (MEXT)
and
Information Mobility Project (CREST, JST)

Objectives

The rapid growth of electronic scientific literature in biology is providing increasingly attractive opportunities for text mining. At the same time, the increasing volume of papers and fact databases available at distributed sources requires a systematic approach for their integration.
Recent development in NLP/IR technologies such as Information Extraction, Term recognition, Concept-based IR, Text Mining, etc. will certainly help biologists to access the relevant information and to discover new facts from huge collections of documents. Some research groups have already launched research projects for text processing and mining in the field of biology.
As the experience of NLP in other fields shows, the success of NLP/IR requires concerted collective efforts of formulating clear research targets, defining evaluation criteria, and building linguistic resources such as correctly annotated texts, ontology and thesauri of terms in the fields, etc.
In order for techniques of NLP, Text Mining and knowledge-based systems to be relevant to application in the biology domain, we believe that it will be extremely fruitful for researchers in biology, knowledge-based systems and NLP to meet to (1) formulate common goals and research targets, and (2) launch concerted efforts for building necessary resources.

The date and venue of the Workshop and the Public Lectures

Date: 18th to 20th, February, 2002
- Workshop: 18th to the morning of 20th
- Public Lectures: Afternoon, 20th
Venue: Tokyo Garden Palace Holel
- 1-7-5 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
- TEL: +81-3-3813-6211

Issues to be discussed

The following are a list of topics to be discussed at the workshop. We will assign each invited speaker to one of these topics, and for each topic we will have one or two sessions, depending on the number of speakers. One session will be for 2 hours, in which we have three talks (30 minutes for each talk, followed by discussion).

(1) Sessions on "Possible targets of NLP research in Biology": The invited speakers in these sessions will have been involved in bio-informatics research projects and think that they could benefit from contributions by NLP researchers.
(2) Sessions on "The current state of the arts of NLP": The invited speakers who give talks here will have been involved in NLP research projects and think that their research can contribute to bio-informatics applications.
(3) Sessions on "Reports on projects of NLP in Biology": The invited speakers in these sessions will have already achieved some research results in research of NLP for biology or are in the process of formulating concrete projects in the field.
(4) Sessions on "Resource and Ontology building for NLP in Biology": The invited speakers in these sessions will have been involved in resource building that they think will contribute to the field.
(5) Sessions on "Possible co-operations among researchers in NLP, knowledge-based engineering and biology": The invited speakers who contribute to this session would like to talk about possible targets or forms of co-operation.

Tentative Time Table

Monday 18th February: The Room "MIYABI" (2nd Floor)

10:00-12:00 Session 1
12:00-13:00 Lunch
13:00-15:00 Session 2
15:00-15:15 Coffie break
15:15-17:15 Session 3
18:00-20:00 Banquet : The Room "SUMA" (2nd Floor)

Tuesday 19th February: The Room "HEIAN" (3rd Floor)

10:00-12:00 Session 4
12:00-13:00 Lunch
13:00-15:00 Session 5
15:00-15:15 Coffie break
15:15-17:15 Session 6
18:30-20:30 Birds-of-a-feather

Wednesday 20th February: The Room "NISHIKI" (2nd Floor)

10:00-12:00 Session 7
12:00-13:00 Lunch
13:00-17:00 Public Lectures: The Room "MIYABI" (2nd Floor)

Photo Gallery

Organizing Committee

Prof. Jun'ichi Tsujii ( Project Leader of Information Mobility Project, Department of Computer Science, University of Tokyo)
Prof. Toshihisa Takagi (Project Leader of Genome Information Science Project, Institute of Medical Science, University of Tokyo)
Dr. Tomoko Ohta (Department of Computer Science, University of Tokyo)
Dr. Yuka Tateishi (Department of Computer Science, University of Tokyo)
Dr. Takako Takai (Institute of Medical Science, University of Tokyo)
Prof. Susumu Goto (Institute for Chemical Research, Kyoto University)
Prof. Kenji Satou (Japan Advanced Institute of Science and Technology)

Invited Speakers from Abroad

Dr. Goran Nenadic (Salford University, UK)
Dr. Lynette Hirschman (the Mitre Corp, USA)
Prof. Udo Hahn (University of Freiburg, Germany)
Dr. Kevin Cohen (University of Colorado, USA)
Prof. Jong C Park (KAIST, Korea)
Prof. Peter Tonellato (Medical College of Wisconsin, USA)
Dr. Dietrich Schuhmann (LION, Germany)
Dr. Alfonso Valencia (CNB-CSIC, Spain)
Dr. Hinrich Schuetze (Novation Biosciences & Stanford University, USA)
Dr. Jerry Hobbs (SRI, USA)
Dr. W.John Wilbur (NCBI, USA)
Prof. Mark Craven (University of Wisconsin, USA)
Prof. Vasileios Hatzivassiloglou (Colombia University, USA)
Prof. Robert P. Futrelle (Northeastern University, USA)
Dr. Thomas S. Morton (University of Pennsylvania, USA)
Dr. See-Kiong Ng (Kent Ridge Digital Laboratories, Singapore)
Dr. Su Jian (Kent Ridge Digital Laboratories, Singapore)

Participants from Japan

Prof. Jun'ichi Tsujii (Graduate School of Information Science and Technology, University of Tokyo)
Prof. Toshihisa Takagi (Institute of Medical Science, University of Tokyo)
Dr. Hidemasa Bono (Genomic Science Center, RIKEN)
Dr. Koichi Doi (Graduate School of Information Science, NAIST)
Dr. Tomaz Erjavec (Graduate School of Information Science and Technology, University of Tokyo)
Prof. Susumu Goto (Institute for Chemical Research, Kyoto University)
Dr. Ken-ichiro Fukuda (Computational Biology Research Center, CBRC)
Mr. Tadayoshi Hara (Department of Information Science, University of Tokyo)
Dr. Teruyoshi Hishiki (Functional Genomics Group, JBIRC)
Dr. Junko Hosaka (Genomic Science Center, RIKEN)
Mr. Jun'ichi Kazama (Graduate School of Information Science and Technology, University of Tokyo)
Dr. Jin-Dong Kim (Graduate School of Information Science and Technology, University of Tokyo)
Mr. Katsuya Masuda (Department of Information Science, University of Tokyo)
Prof. Yuji Matsumoto (Graduate School of Information Science, NAIST)
Dr. Hideki Mima (Graduate School of Information Science and Technology, University of Tokyo)
Dr. Yusuke Miyao (Graduate School of Information Science and Technology, University of Tokyo)
Prof. Shinichi Morishita (Graduate School of Complexity Science and Engineering, University of Tokyo)
Dr. Akiko Murakami (Tokyo Research Labolatory, IBM Japan Co., Ltd.)
Prof. Hiroshi Nakagawa (Information Technology Center, University of Tokyo)
Dr. Yoshio Nakao (Fujitsu Laboratories Ltd.)
Dr. Takashi Ninomiya (Graduate School of Information Science and Technology, University of Tokyo)
Dr. Kiyoshi Nitta (Celestar Lexico-Sciences, Inc.)
Dr. Yoshiki Niwa (Central Research Laboratory, Hitachi Ltd.)
Prof. Kousaku Okubo (Functional Genomics Group, JBIRC)
Mr. Ryosuke Ohniwa (Graduate School of Biostudies, Kyoto University)
Dr. Tomoko Ohta (Graduate School of Information Science and Technology, University of Tokyo)
Dr. Naotaka Ono (Institute of Medical Science, University of Tokyo)
Mr. Satoshi Shimpuku (Graduate School of Information Science and Technology, University of Tokyo)
Dr. Takako Takai (Institute of Medical Science, University of Tokyo)
Prof. Akihiko Takano (Software Research Division, NII)
Dr. Koichi Takeda (Tokyo Research Labolatory, IBM Japan Co., Ltd.)
Dr. Yuka Tateishi (Graduate School of Information Science and Technology, University of Tokyo)
Dr. Yoshimasa Tsuruoka (Graduate school of Frontier Sciences, University of Tokyo)
Dr. Naohiko Uramoto (Tokyo Research Labolatory, IBM Japan Co., Ltd.)
Dr. Duo Wang (Graduate School of Information Science and Technology, University of Tokyo)
Ms. Akane Yakushiji (Graduate School of Information Science and Technology, University of Tokyo)
Ms. Kaoru Yamamoto (Graduate School of Information Science, NAIST)
Prof. Masatoshi Yoshikawa (Graduate School of Information Science, NAIST)

Access to Tokyo Garden Palace Hotel

If you use Airport Limousine from Narita Airport to TCAT (55mins with JP\2,900), and it will take 40 minutes by taxi.
If you use Airport Limousine from Narita Airport to Tokyo Station (80mins with JP\3,000), and it will take 15 minutes by taxi.
If you use Airport Limousine from Narita Airport to Tokyo Dome Hotel (90minutes with JP\3,000), and it will take 5 minutes by taxi and/or 15minutes on foot.
* Please refer to the Airport Limousine site.

For Further Informaition

Contact Office Attn: Mr. Toshio Sumita and Ms. Atsuko Nakamura
c/o Inter Group Corp., Akasaka Dai-ichi Bldg., 4F, 4-9-17 Akasaka, Minato-ku, Tokyo 107-8486, Japan
Phone: +81-3-3479-5131 Fax: +81-3-3423-1601
E-mail: sec-tky3 at intergroup.co.jp

The pages were last updated on the 8th March 2002 by Tomoko OHTA.

Department of Information Science, Faculty of Science, University of Tokyo,
Hongo 7-3-1, Bunkyo-ku, Tokyo 113, Japan.