| name | vmh |
| description | Virtual Metabolic Human (VMH) database — human and gut microbiome metabolism integrated with nutrition and disease knowledge for GEM interpretation. Use when: (1) Contextualizing gapseq / AGORA-style models, (2) Linking metabolites, microbes, and nutrition, (3) Browsing human–microbiome metabolic resources. Portal: https://www.vmh.life. Pair with gapseq for reconstruction; do not treat VMH entries as measured fluxes in your sample.
|
| license | MIT |
| category | utilities |
| tags | ["VMH","GEMs","metabolism","database","gut"] |
| upstream | https://www.vmh.life |
Virtual Metabolic Human (VMH)
Portal: https://www.vmh.life
Citation
Noronha, A. et al. The Virtual Metabolic Human database: integrating human and
gut microbiome metabolism with nutrition and disease. Nucleic Acids Res.
47, D614–D624 (2019). https://doi.org/10.1093/nar/gky992
See also docs/references.md.
Analytical thinking
VMH is a knowledge/integration database (human + gut microbial metabolism,
nutrition, disease links), not a shotgun profiler. Use it to interpret
genome-scale models and metabolites after gapseq (or related GEM tools).
| Resource | Role |
|---|
gapseq | Build/fill models from your genomes/MAGs |
vmh | Browse/integrate human–microbiome metabolic knowledge |
kegg / dram | Pathway annotation alternatives |
Decision tree
Metabolic modeling need?
├─ Reconstruct model from MAG → gapseq
├─ Interpret vs human/gut/nutrition knowledge → vmh
├─ Distill annotations without full GEM → dram
└─ KO maps → kegg (license)
Related skills
gapseq · dram · kegg · public-databases · microbial-mining
