Fig. 1
From: Automated generation of genome-scale metabolic draft reconstructions based on KEGG
General workflow of the AutoKEGGRec pipeline. KEGG organism ID(s) are needed as input to the function (leftmost green box), and optional flags may be set (yellow boxes). Using KEGG IDs to fetch relevant data from the KEGG database and handle them within the pipeline, (1) all links between EC numbers and their genes and (2) the further linkage between EC numbers and reactions (2) are stored. From this information, (3) an Organisms-Reactions-Genes matrix is constructed. (4) Reactions are filtered by e.g. removing polymerization or generic reactions. A first draft consolidated model reconstruction is returned (rightmost green box)