Updating Database ID mapping dictionaries

The mergem algorithm uses database ID mapping dictionaries to map model metabolite identifiers into an internal identifier that allows for comparison and merging of metabolites. Updating the mapping dictionary involves downloading the latest identifier information from databases such as SEED, MetaNetX, KEGG, etc and linking identifiers across databases if they represent the same metabolite, after checking for matching properties. The update process can take a few hours and depends on the internet connection.

The -up argument can be used to update the ID mapping pickles on the command line:

mergem -up

When importing mergem into a python script, the update_id_mapper() function can be called to update the mappping dictionaries as shown below:

import mergem

mergem.update_id_mapper()