- Article -
| In Silico Biology 4, 0007 (2003); ©2003, Bioinformation Systems e.V. |
FREX: a query interface for biological processes with hierarchical and recursive structures
Ken Ichiro Fukuda1,*, Yuki Yamagata2 and Toshihisa Takagi3
1Computational Biology Research Center (CBRC), National Institute of Advanced Industrial
Science and Technology (AIST), 2-43 Aomi, Koutou-ku, Tokyo 135-0064, Japan
Email: fukuda-cbrc@aist.go.jp
2Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), 3-14-4 Shirokane-dai, Minato-ku, Tokyo 108-0071, Japan
Email: snowfox@hgc.jp
3Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
Email: tt@k.u-tokyo.ac.jp
* corresponding author
Edited by E. Wingender; received August 31, 2003; revised and accepted January 23, 2004; published February 22, 2004
Abstract
An intelligent system for signal transduction pathways and other higher order functional knowledge is presented. Molecular mechanisms of biological processes are typically represented as diagrams ("pathways") that have a graph-analogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and range from metal ion to protein to biological processes in general. In addition, the kinds of interactions that connect biological entities are likewise diverse. Consequently, current knowledge about pathways is highly heterogeneous both in the sense of the types of constituents and the granularity of descriptions. To cope with this problem, the proposed system adopts a recursive and hierarchical representation model that enables the annotation and query of pathways or sub-pathways of arbitral granularity. By combining the use of this hierarchical structure and biological ontologies, literature-based information regarding biological mechanisms becomes accessible by computer.
Key words: pathway database, ontology, signal transduction, textual knowledge