Table 2 Representative GEM databases

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]