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The basic graph layout technique, one of many visual- ization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desir- ability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the character- istics and patterns of duplicate and shared vertices, which is crucial for bioinformatics software developers. In this paper, we provide the results of parsing KEGG XML files from a graph-theoretical perspective, for future research in the area of automatic layout techniques in biological pathway domains.

Parsing KEGG XML Files to Find Shared and Duplicate Compounds Contained in Metabolic Pathway Maps: A Graph-Theoretical Perspective