Reaction, Metabolite, and Gene Annotations

• Human-GEM provides annotation information and external identifiers for model components of reactions, metabolites and genes in tsv files under the model/ directory.

• These files can be directly edited on the web or via text editor for curations. They can also be imported/exported to/from MATLAB using the importTsvFile and exportTsvFile functions provided by Human-GEM.

• The structures of these tsv files are tabulated below.

  • reactions.tsv content:

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.tsv` content:

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.tsv` content:

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