Fig. 1

A phylogenetic tree of all of the GEMs reconstructed to date at the family level. GEMs for 434, 40, and 117 taxonomic families of bacteria (light blue), archaea (light purple), and eukarya (pink), respectively, are marked in the phylogenetic tree. Organism names are labeled with circles of different colors outside the circular phylogenetic tree, depending on the development methods used: manual, Path2Models [13], AGORA [14], and CarveMe [15]. For manually reconstructed GEMs, the relevant PubMed identifier (PMID) or digital object identifier (DOI) for the latest GEM version is additionally indicated. The phylogenetic tree was prepared as follows. First, organism names were collected from BioModels for the GEMs from Path2Models, from Virtual Metabolic Human (VMH) for AGORA models, and from a GitHub repository (https://github.com/cdanielmachado/embl_gems/blob/master/model_list.tsv) for CarveMe. Next, National Center for Biotechnology Information (NCBI) taxids at the species level and taxonomic lineages for all of the organisms subjected to the GEM reconstruction were obtained from a dataset available (as of May 14, 2019) at the NCBI Taxonomy FTP (ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz). Finally, a Newick file for all of the organisms with taxids was subsequently generated using an in-house Python script at the family level, and this file was used to create a phylogenetic tree using iTOL (https://itol.embl.de/) [16]. A phylogenetic tree of GEMs at the species level is available as Additional file 1. A full list of organisms subjected to the GEM reconstruction and preparation of phylogenetic trees is available as Additional file 2