This directory contains the Human-GEM model and annotation files.
The model is available as .xml, .xlsx, .txt, .yml, and .mat. Note that only the .yml version is available on branches other than main (e.g., develop), to facilitate tracking of model changes.
Additional annotation information and external identifiers for Human-GEM reactions, metabolites, and genes are provided as tsv files. The structure of the tsv files are tabulated below.
reactions.tsvcontent:
| fieldname | annotation |
|---|---|
| rxns | identical to model.rxns |
| rxnKEGGID | KEGG reaction ID |
| rxnBiGGID | BiGG reaction ID |
| rxnEHMNID | EHMN reaction ID |
| rxnHepatoNET1ID | HepatoNET1 reaction ID |
| rxnREACTOMEID | REACTOME ID |
| rxnRecon3DID | Recon3D reaction ID |
| rxnMetaNetXID | MetaNetX reaction ID |
| rxnHMR2ID | HMR2 reaction ID |
| rxnRatconID | Ratcon reaction ID |
| rxnTCDBID | TCDB ID |
| spontaneous | Spontaneous status |
| rxnMAID | MA reaction ID |
| rxnRheaID | Rhea ID |
| rxnRheaMasterID | Master Rhea ID |
metabolites.tsvcontent:
| fieldname | annotation |
|---|---|
| mets | identical to model.mets |
| metsNoComp | model.mets without compartment suffix |
| metBiGGID | BiGG metabolite ID |
| metKEGGID | KEGG metabolite ID |
| metHMDBID | HMDB ID |
| metChEBIID | ChEBI ID |
| metPubChemID | PubChem ID |
| metLipidMapsID | LipidMaps ID |
| metEHMNID | EHMN metabolite ID |
| metHepatoNET1ID | HepatoNET1 metabolite ID |
| metRecon3DID | Recon3D metabolite ID |
| metMetaNetXID | MetaNetX metabolite ID |
| metHMR2ID | HMR2 metabolite ID |
| metMAID | MA metabolite ID |
genes.tsvcontent:
| fieldname | annotation |
|---|---|
| genes | Ensembl gene ID |
| geneENSTID | Ensembl transcript ID |
| geneENSPID | Ensembl protein ID |
| geneUniProtID | UniProt ID |
| geneSymbols | Gene Symbol |
| geneEntrezID | NCBI Entrez ID |
| geneNames | Gene Name |
| geneAliases | Alias Names |
To import/export this annotation data to/from MATLAB, use the importTsvFile and exportTsvFile functions, respectively.