期刊
BMC SYSTEMS BIOLOGY
卷 4, 期 -, 页码 -出版社
BMC
DOI: 10.1186/1752-0509-4-114
关键词
-
资金
- Engineering and Physical Sciences Research Council (EPSRC)
- Biotechnology and Biological Sciences Research Council (BBSRC) [BB/F006012/1]
- Biotechnology and Biological Sciences Research Council [BB/F006012/1] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [EP/E036252/1] Funding Source: researchfish
- BBSRC [BB/F006012/1] Funding Source: UKRI
- EPSRC [EP/E036252/1] Funding Source: UKRI
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.
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