==General== This folder contains data required for Architect's model reconstruction module. The first time Architect is run in this capacity, a number of files are created, and will populate a number of the folders here. Please do not manipulate (delete, add or modify) any files or folders here, as this may lead to unexpected behaviour at runtime. ==More details== Architect performs model reconstruction using reaction definitions either from KEGG or from BiGG (including information used by the CarveMe reconstruction tool). The information in the folders here contain partial information from these reaction databases. Information relevant to BiGG is found in the folders with the word "BiGG". Information from the BiGG database was utilized, along with curated information from CarveMe's reaction databases. BiGG can be accessed here: http://bigg.ucsd.edu/ More information about CarveMe can be accessed here: https://carveme.readthedocs.io/ The folder KEGG_universe contains a list of reactions and compounds of interest for KEGG's reaction database. The first time model reconstruction is being performed, information from KEGG is downloaded (using its API) and deposited in this folder. The KEGG database can be accessed here: https://www.genome.jp/kegg/pathway.html The folder MetaNetX is empty until the first time model reconstruction is performed; at this point, information from MetaNetX is downloaded. This information is utilized to provide database links from KEGG and BiGG identifiers to other databases in the SBML output. The MetaNetX database can be accessed here: https://www.metanetx.org/ ==Relevant publications== D. Machado et al, "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities", Nucleic Acids Research, gky537, 2018. doi: https://doi.org/10.1093/nar/gky537 C. J. Norsigian et al, "BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree", Nucleic Acids Research, gkz1054, 2020. doi: https://doi.org/10.1093/nar/gkz1054 M. Kanehisa et al, "KEGG: new perspectives on genomes, pathways, diseases and drugs", Nucleic Acids Research, gkw1092, 2016. doi: https://doi.org/10.1093/nar/gkw1092 S. Moretti et al, "MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models", Nucleic Acids Research, gkaa992, 2021. doi: https://doi.org/10.1093/nar/gkaa992 ==License== CarveMe is released under an Apache License (included here). The license information for the BiGG Models website can be found at: http://bigg.ucsd.edu/license. The data available from the MetaNetX database is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).