Computational Biology Research Center[CBRC]

MISSION

INOH Project: Development of Database
for High-Order Knowledge

MEMBERS

Ken Fukuda : CBRC

Interview : 7th Sep. 2007

INOH: Pathway Data Representation and Ontology

Now that the deciphering process for human and mouse genomes has been completed, there has been increased momentum for the creation of a database for relationship combinations that express how proteins interact with each other and establish molecular mechanisms in life phenomena - or in other words, pathway knowledge. The real issue, however, is how to process this information via computer.

Pathway knowledge is comprised of a variety of elements (concepts), such as compounds, proteins, metallic ions, and life phenomena including cellular death. There are also many types of relationships that exist between these elements, such as transmission, modification, regulation, and biochemical reactions. When creating a database that catalogs knowledge comprised of heterogeneous elements that interact in complex ways, we need to remain strongly conscious of ontology. Against this backdrop, Dr. Fukuda's approach to this project incorporates the four missions previously mentioned, specifically the development of computer processing technology for high order knowledge related to the field of molecular biology; gathering of high order knowledge from the literature produced by specialists; facilitation of required ontologies; and construction of a comprehensive pathway database incorporating the development of a pathway database system.

BioPAX Ontology

At present it is thought that there are over 240 pathway databases, including those used both for commercial and non-commercial purposes. These databases are constructed using differing frameworks in accordance with the type of knowledge targeted and the purpose a given database serves. The databases are not built using a unified data format, and so bringing data together from multiple databases, and processing the gathered data with separate pathway data analysis software would be prohibitively expensive, as conversion programs for importing and exporting data of differing formats would need to be developed for each format. As a result, the volume of pathway data utilized broadly as a knowledge platform pales in comparison with the actual amount of data that has been digitized. The development of a common data conversion format that can accurately and comprehensively express information from each database is extremely desirable. A group known as BioPAX has been established to realize this desire. Dr. Fukuda participates in this community effort as a primary data provider and is a member of the core working group.

Summary

Since 2003 Dr. Fukuda led the INOH Project and participated as an integral member of BioPAX, and acted as chairperson of the executive board when the first BioPAX International Symposium and the BioPAX Specification Formulation Meeting were held at CBRC in 2004. Many of the items proposed by the INOH Project have been employed within specifications formulated by BioPAX. The success of the INOH Project has exceeded initial expectations, and it is now recognized to pathway database developers/analysts and ontology developers worldwide.