Genomics Inform.  2008 Sep;6(3):147-152.

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

• Kang SH
• Jang MH
• Whang J
• Park HS

Abstract

The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability 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 characteristics 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.

Keyword

drawing algorithm; XML; metabolic pathway; scale-free network

MeSH Terms

Computational Biology
Metabolic Networks and Pathways
Systems Biology