Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process.
DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga, M., & Best, A. (2007). Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics, 8. https://doi.org/10.1186/1471-2105-8-139