Abstract
Genome-scale model reconstruction represents a major tool in the field of Metabolic Engineering .This paper reports on a study about data integration issues in the process of genome-scale reconstruction of the metabolic model of the bacterium Zymomonas mobilis, a promising organism for bioethanol production. Data is retrieved from the Entrez Gene, KEGG, BioCyc and Brenda databases, and the several processes involved in data integration from these sources are described, as well as the data quality issues.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Rocha, I., Forster, J., Nielsen, J.: Design and application of genome-scale reconstructed metabolic models. Methods Mol. Biol. 416, 409–431 (2008)
Notebaart, R.A., van Enckevort, F.H., Francke, C., Siezen, R.J., Teusink, B.: Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (7), 296 (2006)
Seo, J.S., Chong, H., Park, H.S., Yoon, K.O., Jung, C., Kim, J.J., Hong, J.H., Kim, H., Kim, J.H., Kil, J.I., Park, C.J., Oh, H.M., Lee, J.S., Jin, S.J., Um, H.W., Lee, H.J., Oh, S.J., Kim, J.Y., Kang, H.L., Lee, S.Y., Lee, K.J., Kang, H.S.: The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat. Biotechnol. 1(23), 63–68 (2005)
Tsantili, I.C., Karim, M.N., Klapa, M.I.: Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis. Microb.Cell Fact. (6), 8 (2007)
Borodina, I., Nielsen, J.: From genomes to in silico cells via metabolic networks. Curr. Opin. Biotechnol. 3(16), 350–355 (2005)
GOLD (Genomes OnLine Database v 2.0) web site (2008), http://www.genomesonline.org/
TIGR web site. TIGR web site (2008)
NCBI web site. NCBI web site (2008)
BRENDA web site. BRENDA web site (2008)
KEGG (Kyoto Encyclopedia of Genes and Genomes) web site (2008), http://www.genome.jp/kegg/
NCBI’s Entrez Gene Web site (2008), http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
Minorou, K., Susumu, G.: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 1(28), 27–30 (2000)
Minorou, K., Michihiro, A., Susumu, G., Masahiro, H., Mika, H., Masumi, I., Toshiaki, K., Shuichi, K., Shujito, O., Toshiaki, T., Yoshihiro, Y.: KEGG for linking genomes to life and the environment. Nucleic Acids Research 36 (2007)
BRENDA introduction. BRENDA web site (2008)
Schomburg, I., Chanf, A., Hofmann, O., Ebeling, C., Ehrentreich, F., Schomburg, D.: BRENDA: a resource for enzyme data and metabolic information. TRENDS in Biochemical Sciences 1(27), 54–56 (2002)
Schomburg, I., Chang, A., Schomburg, D.: BRENDA, enzyme data and metabolic information. Nucleic Acids Research 1(30), 47–49 (2001)
BioCyc Introduction. BioCyc web page (2008)
Karp, P., Ouzounis, C., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V., López-Bigas, N.: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 19(33) (2005)
CHEBI web site. CHEBI web site (2008)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Pinto, J.P. et al. (2009). Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis . In: Corchado, J.M., De Paz, J.F., Rocha, M.P., Fernández Riverola, F. (eds) 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008). Advances in Soft Computing, vol 49. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85861-4_12
Download citation
DOI: https://doi.org/10.1007/978-3-540-85861-4_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85860-7
Online ISBN: 978-3-540-85861-4
eBook Packages: EngineeringEngineering (R0)