Addition of KEGG Pathways

Warning

Will be deprecated from version 2.0.0 onwards.
Functions have been moved to refinegems.curation.pathways.

The KEGG database holds information on metabolic pathways. You can use this module 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>)