Addition of KEGG Pathways

The KEGG database holds information on metabolic pathways.

Add KEGG pathways from reaction:

You can use this to add KEGG pathways with the libSBML Groups plugin.

The workflow of the script is as follows:

  1. Extraction of the KEGG reaction IDs from the annotations of your reactions

  2. Identification, in which KEGG pathways these reactions occur

  3. Addition of all KEGG pathways for a reaction with the biological qualifier OCCURS_IN to the annotations

  4. Addition of all KEGG pathways as groups with references to the contained reactions as groups:member

The only function that you will need to access is kegg_pathways():

1import refinegems as rg
2model_pathway_groups, non_kegg_reactions = rg.pathways.kegg_pathways(<path to your model>)
3rg.io.write_to_file(model_pathway_groups, <path to modified model>)