Simulative representation of biological knowledge using object-oriented database language

Makoto Hirosawa[1] (
Reiko Tanaka[2] (
Hidetoshi Tanaka[3] (
Masayuki Akahoshi[3] (
Masato Ishikawa[3] (

[1] Kazusa DNA Research Institute
1532-3 Yana-Uchino, Kisarazu, Chiba 292 Japan
[2] Information and Mathematical Science Laboratory, Inc.
2-43-1 Ikebukuro, Toshima-ku, Tokyo 171 JAPAN
[3] Institute for New Generation Computer Technology (ICOT)
1-4-28-21F Mita, Minato-ku, Tokyo 108 JAPAN


Major advances in bio-technology enable us to describe various phenomena occuring in the body using the language of genes and proteins. It is important to represent these phenomena in knowledge base, and to visualize them properly. The visualization of the phenomena with reference to related databases facilitates research on genes.
As the first step in realizing a database like the one stated above, we have studied the representation of biological knowledge needed to describe biological phenomena and have developed a prototype knowledge base. The knowledge base is described in micro-Quixote, an object-oriented database language executable on Unix. The knowledge base can cover the knowledge related to signal transduction within a cell and that related to transcription of genes.
In our prototype system, a sort of simulation can be done. With the arrival of a signaling ligand at the surface of a cell, proteins along suitable pathways are activated in our simulated cell. As a consequence of series of activations(a chain of inferences), some biological responses are deduced and shown to users.