Maintenance of Transcription Factor DataBase TFDBby TFDB Maintenance System
Masako Kaizawa 14
Satoru Watanabe 2
Takahiro Nobukuni 3
mkaizawa@info.ncc.go.jp
stwatana@gan2.ncc.go.jp
tnobukun@gan2.ncc.go.jp
Masami Horikoshi 5
Hiroshi Handa 6
Yoshiyuki Kuchino 2
horikosh@gene.selector.trc-net.co.jp
hhanda@bio.titech.ac.jp
ykuchino@ncc.go.jp
3
1
Takao Sekiya
Hiroshi Mizushimatsekiya@ncc.go.jp

hmizushi@ncc.go.jp

1

Cancer Information and Epidemiology Division, National Cancer Center Research

2

InstituteBiophysics Division, National Cancer Center Research Institute

3456Oncogene Division, National Cancer Center Research Institute5-1-1 Tsukiji, Chuo-ku, Tokyo 104, Japan
System Science Department, Mitsubishi Research Institute, Inc.
2-3-6 Otemachi Chiyoda-ku, Tokyo 100, Japan
Horikoshi Gene Selector Pro ject, Exploratory Research for Advanced Technology
5-9-6 Tokodai, Tsukuba, Ibaraki, JapanTokyo Institute of Technology, Graduate School of Bioscience and Biotechnology
4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan

1 Introduction
TFD [1]{[4] was a very useful and required database for molecular biologists analyzing transcription
mechanisms and gene expressions, which was maintained by David Ghosh at NCBI until 1993. We took
over his work as TFDB (which is based upon the `sites' table of the TFD [6, 7]), and we established
TFDB Maintenance System described in [5] which gathers transcription factor data from articles, toupdate TFDB systematically.
We started the maintenance of TFDB with this TFDB Maintenance System using many journals
which we can obtain from MEDLINE database. In this paper, we describe how we maintain the TFDBusing this system.

2 System
contains the following subsystems: (1) Information Retrieval Subsystembased on retrieval engine described in [8] which collects references related to transcription factor fromMEDLINE correctly and eciently, (2) Information Extraction Subsystem described in [5, 8] which
extracts candidates of `transcription factors' and `target(transcription factor binding) sequences' fromthe result of Information Retrieval Subsystem, and (3) Data Registration Subsystem [5] which enables
to register new data easily and interactively on WWW (the interface of Data Registration Subsystem,
see Fig. 1).

TFDB Maintenance System

3 Method
We are maintaining TFDB by the following method. (1) Collecting abstracts of the various elds,
published in 1990 { 1998 from MEDLINE database as a text data format. (2) Scoring abstracts related
to the transcriptional regulation using Information Retrieval Subsystem. (3) The words related to316

Figure 1: TFDB Data Registration interface and new data of TFDB.
transcription factors

and its binding sequences are automatically extracted from (2) with Information. (4) Specialist authorizes the validity of (3) and register with Data Registration

Extraction Subsystem.

Subsystem

4 Results and Discussion
We used 265,249 abstracts for the purpose of trying the performance of the TFDB Maintenance
System. We chose the top 150 abstracts from the output result of Information Retrieval Subsystem.
All of the 150 abstracts related to transcriptional regulatory mechanisms. About 7 candidatesof binding factor and about 1:6 candidates of binding sequence appeared per abstract in average.
Analysis of experts selection resulted that 10% of the top 150 abstracts contains new TFDB data withBinding Sequences.
We can collect data related to transcription factors eciently with Information Retrieval subsystem and extract candidate of `Binding Factors', `Binding Sequences' very easily with Information
Extraction subsystem. We are now continually authorizing the extracted data with Data Registration
Subsystem.
This system is also suitable for maintaining databases in other elds.

Acknowledgements
We thank Dr. Sarai (The Institute of Physical and Chemical Research, GENE BANK) for giving us
advices about this system. This work was supported in part by a Grant-in-Aid for Scienti c Research
on Priority Areas, `Genome Science', from the Ministry of Education,Science, Sports and Culture inJapan.

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References[1] Ghosh, D., A relational database of transcription factors, Nucleic Acid Research, 18:1749{1456,1990.
[2] Ghosh, D., New developments of a transcription factors database , Trends in Biochemical Sciences, 16:455{457, 1991.
[3] Ghosh, D., TFD:the transcription factors database, Nucleic Acid Research, 20S:2091{2093, 1992.
[4] Ghosh, D., Status of the transcription factor database (TFD), Nucleic Acid Research, 21S:3117{3118, 1993.
[5] Kaizawa, M., Okazaki, T., and Mizushima,H., Establishment of Transcription Factor DataBase
TFDB Maintenance System, Genome Informatics 1997, Universal Academy Press, 292{293, 1997.
[6] Mizushima, H., Establishment of a Program for Searching Transcription Factor Binding Region,and Analysis of tRNA/Gln Gene, Proceeding of 15th Japanese Molecular Biology Meeting, 1992.
[7] Mizushima, H., Hayashi, K., Establishment of Transcription Factor Database and Human Mutation Database, Proc. Genome Informatics Workshop 1994, Universal Academy Press, 142{143,1994.
[8] Ohta, Y., Yamamoto, Y., Okazaki, T., Uchiyama, I., and Takagi,T., Automatic Construction ofKnowledge Base from Biological Papers, Proc. 5th International Conference on Intelligent Systemfor Molecular Biology (ISMB '97), 218{225, 1997.
[9] Okazaki, T., Kaizawa, M., and Mizushima,H., Establishment and Management of Transcription
Factor DataBase TFDB, Genome Informatics 1996, Universal Academy Press, 218{219, 1996.

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