Abstract
The basic graph layout technique, one of the visualization techniques, deals with the problem of positioning the vertices in a way to maximize understandability and usability in a graph. This technique is becoming a vital part for further development 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 characteristics 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 layout techniques in large-scale biological pathway domain.
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