A statistical analysis of relation degree of compound pair on online biological pathway databases

Abstract

The basic graph layout technique, one of the visualization te chniques, deals with the problem of positioning the vertices i n a way to maximize understandability and usability in a grap h. This technique is becoming a vital part for further develop ment in the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genome scale flow of metabolism requires understanding of the charac teristics of metabolites and reactions, which suggest valuable information to bioinformatics software developers for better visualization of automatic graph layout. In this paper, we define the term relation degree of a compound pair to provide a reasonable way to visualize metabolic pathway atlas, based on the parsing result of the publicly available XML files. It is a preliminary step for future research in the area of automatic 1 ayout techniques in large-scale biological pathway domain. Copyright 2009 ACM.