What are the GEMs used for taxon-metabolite interaction network?

Genome-scale metabolic models (GEMs) are reconstructions of the metabolic networks which can serve as a scaffold for multi-omics data integration. OmicsNet mainly leverages GEMs of human gut microbes from two databases:

  • AGORA (assembly of gut organisms through reconstruction and analysis) is a collection of GEMs for 818 human gut microbes, the detailed reconstruction method can be found Stefanía Magnúsdóttir, et al..
  • EMBL GEMs are built for all reference and representative bacterial genomes of NCBI RefSeq (release 84) using CarveMe(Daniel Machado, et al.), 1288 of which are annotated as human gut microbes.