Computational Biology Research Center[CBRC]

MISSION

INOH Project: Development of Database
for High-Order Knowledge

MEMBERS

Ken Fukuda : CBRC

Interview : 7th Sep. 2007

An unparalleled amount of knowledge and information has been produced in the field of biology over the last few years. Knowledge and information gained by researchers becomes public through academic articles, and the sheer volume of written documentation produced is enormous. Searching through all of this information and knowledge and extracting meaning from a biological context has become a very arduous task. Another concern is that different researchers use differing terminology when explaining the same concept, leading to a lack of consistency in expression. The content of ideas needs to be interpreted accurately when information and knowledge is shared between researchers - if it is not, important ideas and data can become buried and lost within articles. There is a need to create a computer-based database to ensure that this does not happen.

Dr. Ken Fukuda is presently involved with the INOH (Integrating Network Objects with Hierarchies) Project, an initiative that seeks to create a database for high-order knowledge that shares information gleaned from academic articles. In contrast to knowledge relating to the functions of individual substances, high order knowledge refers to knowledge about the functions described in the relationships between substances and substance characteristics. Some examples are the pathways for genes and proteins that regulate cellular function. This project aims to create a database for high order knowledge (signal transduction pathways); Dr. Fukuda says “We want to extract the bountiful knowledge found in academic articles, convert it into data that a computer can recognize, restructure it, and build a database that enables researchers to share this information.”

The INOH Project is divided into four broad missions. The first involves the development of a knowledge processing technology for high order knowledge in biology; the second concerns curation of data received from biologists; the third deals with facilitating ontologies for handling knowledge that we find in scientific literature; and finally, the fourth mission involves the development of a database system for high order knowledge. Dr. Fukuda’s group is currently tackling these issues in a comprehensive manner with the support of BIRD of the Japan Science and Technology Agency (JST). The precursor to the INOH Project began in 2001, and Dr. Fukuda has taken the lead as a co-PI since 2003.