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

Published: 15 February 2009 Publication History

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.

References

[1]
Kaufmann, M., and Wagner, D., (Eds.) (2001) Drawing Graphs: Methods and Models, LNCS 2025, Springer.
[2]
Moritz, Y. B. and Isabel, R. (2001). A graph layout algorithm for drawing metabolic pathways, Bioinformatics, 17(5):461--467.
[3]
Yuan Wang (2008). Familiar Layouts Generation for Metabolic Pathway Graph Visualization, MS Thesis, Case Western Reserve University.
[4]
M. Y. Becker and I. Rojas (2001). A Graph Layout Algorithm for Drawing Metabolic Pathways, BIOINFORMATICS, Vol. 17, No. 5, pp.461--467.
[5]
Karp, P. D. and Paley, S. M. (1994). Automated drawing of metabolic pathways, Proc. of the 3rd Intl. Conference on Bioinformatics and Genome Res., 225--238.
[6]
E. H. Song, M. K. Kim, and S. H. Lee (2006). A Metabolic Pathway Drawing Algorithm for Reducing the Number of Edge.
[7]
M. Kato et al. (2005). Automatic Drawing of Biological Networks Using Cross Cost and Subcommponent Data, Genome Informatics 16(2):22--31.
[8]
Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27--30.
[9]
Moritz Y. Becker and Isabel Rojas. (2000) A graph layout algorithm for drawing metabolic pathways, BIOINFORMATICS, Vol. 17, No 5, pp 461--467.
[10]
Bray, Tim; J. Paoli, C. M. Sperberg-McQueen, E. Maler, F. Yergeau (2006). <Extensible Markup Language (XML) 1.0 (Fourth Edition) - Origin and Goals>. World WideWeb Consortium.
[11]
"XML Definition" SOA Online. 21 Jul 2008 <http://searchsoa.techtarget.com/sDefinition/0,sid26_gci213404,00.html>
[12]
H. C. Purchase, J. Allder, D. Carrington.(2002) Graph LayoutAesthetics in UML Diagrams: User Preference, Journal of Graph Algorithms and Applications, vol.6, no.3, pp. 255--279.
[13]
S. H Kang, M. H Jang, J. Y Whang, and H. S Park(2008). Parsing KEGG XML Files to Find Shared and Duplicate Compounds Contained in Metabolic Pathway Maps: A Graph-Theoretical Perspective, Genomics & Informatics, vol. 6, no. 3 (in press).
[14]
H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai and A.-L. Barabasi (2000). The Large-scale Organization of Metabolic Networks, NATURE, Vol. 407, pp.651--654.
[15]
Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S., and Kanehisa, M. (2008). KEGG Atlas mapping for global analysis of metabolic pathways, Nucleic Acids Res. May 13.
[16]
E. H. Song, S. I. Ham, S. D. Yang, A. Rhie, H. S. Park, and S. H. Lee (2008). J2pathway: A Global Metabolic Pathway Viewer with Node Abstracting Features, Genomics & Informatics, Vol. 6, No. 2, 118--124.

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

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        cover image ACM Conferences
        ICUIMC '09: Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication
        February 2009
        704 pages
        ISBN:9781605584058
        DOI:10.1145/1516241
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        Published: 15 February 2009

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        Author Tags

        1. XML
        2. drawing algorithm
        3. edge crossing
        4. metabolic pathway
        5. parsing
        6. relation degree

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