Kegg

createUniversalReactionModel(KEGGFilename, KEGGBlackList)

Creates the U matrix using the universal data from the KEGG database

USAGE:

KEGG = createUniversalReactionModel (KEGGFilename, KEGGBlackList)

INPUTS:

• KEGGFilename – downloaded from KEGG database (ie. ‘reaction.lst’)

• KEGGBlackList – KEGG reactions not to use

OUTPUT:

KEGG – U Matrix

mapKEGGID2Model(model, Dictionary)

This function matches the compound abreviation in model and from CompAbr and connects with the model metabolite the corresponding KEGGID

USAGE:

model = mapKEGGID2Model (model, Dictionary)

INPUTS:

• model – COBRA model structure with fields:

  • .mets - m x 1 column cell array of metabolite identifiers

• Dictionary – consists of:

  • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)

  • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

model – KEGG model structure with added field:

• .metKEGGID - m x 1 column cell array of KEGG metabolite identifiers, one per entry in model.mets

mapMetName2KEGGID(model, Dictionary)

This function maps names of metabolites to KEGG IDs.

USAGE:

model = mapMetName2KEGGID (model, Dictionary)

INPUTS:

• model – KEGG model structure with fields:

  • .mets - m x 1 column cell array of metabolite identifiers

• Dictionary – consists of:

  • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)

  • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

model – COBRA model structure with added fields:

• .metKEGGID - set equal to the input model.mets (unchanged)

• .metsAbr - m x 1 column cell array of metabolite abbreviations matched via Dictionary, empty where no match is found

transformKEGG2Model(modelKEGG, dictionary)

Translates the metabolites from KEGG to cobra model names.

USAGE:

model = transformKEGG2Model (modelKEGG, dictionary)

INPUTS:

modelKEGG – KEGG model structure

OPTIONAL INPUTS:

dictionary – consists of:

• CompAbr = dictionary(:, 1): List of compounds abreviation (non-compartelized)

• KEGGID = dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

model – COBRA model structure

transformModel2KEGG(model, Dictionary)

Replaces model.mets with model.metKEGGID. If no KEGGID defined, the empty cell will be replaced with metabolite abreviation.

USAGE:

modelKEGG = transformModel2KEGG (model, Dictionary)

INPUTS:

• model – COBRA model structure

• Dictionary – consists of:

  • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)

  • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

modelKEGG – KEGG model structure