Other

populateModelwithRxnIDs(model)[source]

Populates a COBRA model with reaction cross-reference identifiers looked up from a local VMH reaction list spreadsheet and, for rxnSEEDID, from a DEMETER seed-to-VMH translation table.

USAGE:

[modelUpdated] = populateModelwithRxnIDs (model)

INPUTS:

model – COBRA model structure

OUTPUT:

modelUpdated – COBRA model structure with the following reaction ID fields populated (overwritten where already present):

  • .rxnECNumbers - EC number(s) for the reaction

  • .rxnKEGGID - KEGG reaction identifier

  • .rxnMetaNetXID - MetaNetX reaction identifier

  • .rxnSEEDID - ModelSEED reaction identifier

  • .rxnRheaID - Rhea reaction identifier

  • .rxnBRENDAID - BRENDA reaction identifier (same value as .rxnECNumbers)

Note

Allowed COBRA fields can be found here:

fileName = which(‘COBRA_structure_fields.tab’); [raw] = descFileRead(fileName); raw.Model_Field

Reaction ID fields include: rxnGeneMat, rxnConfidenceScores, rxnNames, rxnNotes, rxnECNumbers, rxnReferences, rxnKEGGID, rxnKEGGPathways, rxnMetaNetXID, rxnBRENDAID, rxnBioCycID, rxnReactomeID, rxnSABIORKID, rxnSEEDID, rxnRheaID, rxnBiGGID, rxnSBOTerms