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. 2018 Dec 4;19:467. doi: 10.1186/s12859-018-2472-z

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© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — 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)