Higher Order Knowledge Processing: Pathway Database and Ontologies.

Fukuda,  Ken Ichiro

Genomics Inform > Volume 3(2); 2005 > Article

Review

Genomics & Informatics 2005;3(2): 47-51.

Higher Order Knowledge Processing: Pathway Database and Ontologies.

¹Computational Biology Research Center (CBRC), Japan. fukuda.cbrc@aist.go.jp
²National Institute of AdvaMinireviewnced Industrial Science and Technology (AIST), Japan.
³AIST Tokyo Waterfront Bio-IT Research Bldg. 10F. 42 Aomi, ENutou-ku, Tokyo 135-0064, Japan.

Abstract

Molecular mechanisms of biological processes are typically represented as "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 the semantics is embedded implicitly. The kinds of interactions that connect biological entities are likewise diverse. Consequently, how to model or process pathway data is not a trivial issue. In this review article, we give an overview of the challenges in pathway database development by taking the INOH project as an example.

Keywords: athway database; ontology; signal transduction; textual knowledge