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BMC Syst Biol. 2010 Aug 16;4:114. doi: 10.1186/1752-0509-4-114.

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks.

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  • 1Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

Abstract

BACKGROUND:

Genome-scale metabolic reconstructions have been recognised as a valuable tool for a variety of applications ranging from metabolic engineering to evolutionary studies. However, the reconstruction of such networks remains an arduous process requiring a high level of human intervention. This process is further complicated by occurrences of missing or conflicting information and the absence of common annotation standards between different data sources.

RESULTS:

In this article, we report a semi-automated methodology aimed at streamlining the process of metabolic network reconstruction by enabling the integration of different genome-wide databases of metabolic reactions. We present results obtained by applying this methodology to the metabolic network of the plant Arabidopsis thaliana. A systematic comparison of compounds and reactions between two genome-wide databases allowed us to obtain a high-quality core consensus reconstruction, which was validated for stoichiometric consistency. A lower level of consensus led to a larger reconstruction, which has a lower quality standard but provides a baseline for further manual curation.

CONCLUSION:

This semi-automated methodology may be applied to other organisms and help to streamline the process of genome-scale network reconstruction in order to accelerate the transfer of such models to applications.

PMID:
20712863
[PubMed - indexed for MEDLINE]
PMCID:
PMC2930596
Free PMC Article
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