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m-jahn / genome-scale-models

Genome scale metabolic models in SBML format
GNU General Public License v3.0
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store Bigg reaction and metabolite annotation locally #5

Closed m-jahn closed 4 years ago

m-jahn commented 4 years ago

Currently the complete Bigg annotation for all available reactons and metabolites is downloaded every time the model is updated. It would be much more useful to store are downloaded data locally in a data/ folder. Reference metabolites and reactions downloaded from Bigg could be stored in a plain text format such as an sbml, json, or text file.

The model_upgrade script would then first look locally for annotation, and then download all missing reaction annotations from Bigg, add it to the local reference and save it under data. The new function to do that will be get_bigg_annotation.py.

m-jahn commented 4 years ago

Latest commit 354f5c7 contains the function get_bigg_annotation() that retrieves annotation from Bigg for metabolites and reactions. It stores those in two separate *.json pseudo model files that can be imported again by update_bigg_annotation(). Both functions work for reactions and metabolites.