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Table 2 Representative GEM databases

From: Current status and applications of genome-scale metabolic models

Database Available GEMs URL Reference(s)
BiGG Models 84 high-quality GEMs that were manually reconstructed http://bigg.ucsd.edu [97]
BioModels 6753 patient-specific GEMs using TCGA datasets, > 2600 GEMs from the Path2Models project, and 641 manually curated small-scale metabolic models from the literature http://www.ebi.ac.uk/biomodels [98]
Human Metabolic Atlas (HMA) Two generic and > 100 context-specific human GEMs, five human gut microbiota species GEMs, and a mouse GEM http://www.metabolicatlas.org [99]
MEMOSys 2.0 20 publicly available GEMs in a standardized format http://memosys.i-med.ac.at (unstable) [100]
MetaNetX 217 GEMs collected from GEM-relevant databases (e.g., BiGG Models and Model SEED) in a standardized format http://www.metanetx.org [101]
Model SEED 39 plant GEMs reconstructed using PlantSEED http://modelseed.org [93, 102]
Virtual Metabolic Human (VMH) 818 GEMs for gut microbes (AGORA models) and Recon3D http://www.vmh.life [103]