Metabolite abbreviation of the KGML-based model generation

CARMEN provides three variations to affect the abbreviation of metabolites:
  1. Insert KEGG compound IDs
    KEGG compound IDs can easily associated with their metabolites. Depending on the utilization of a metabolic network, this metabolite abbreviation might be satisfying.

  2. Insert KEGG abbreviations
    For each compound ID one or more alternative names are stored in KEGG. If they are shorter than 10 characters, they will be used as metabolite name. In some cases, this random procedure facilitates the choice of unusual compound names.

  3. Insert user-defined abbreviations
    Compound IDs and self-defined metabolite abbreviations have to be stored in a tab-separated file that can be used by CARMEN. The list can be completed by a user.

Compound name variation

Figure 3: KGML-based glycolysis reconstruction using the option for selecting compound abbreviations (-m 1, 2 or 3).

Download XanthomonasB100_metaboliteDownload SBML file.
Download shortcutsDownload list of compounds and user-defined abbreviations.