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HelikarLab / COMO

Identify drug targets and potentially repurposable drugs for metabolism-impacting diseases
https://helikarlab.github.io/COMO/
GNU General Public License v3.0
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Import common-name metabolites in model creation (step 4) #90

Open JoshLoecker opened 1 year ago

JoshLoecker commented 1 year ago

Movivation

Adding reactions to MADRID can be tedious, because specific reaction names are required.

It would be beneficial to be able to include a common name (i.e., L-glutamine, glutamic acid, etc.) instead of the reaction name currently required by MADRID's model creation step (i.e., EX_gln_L[e])

Using web scraping or an API access for the Human Metabolome Database, it should be possible to obtain reaction information for common-name metabolites

Input

Input would come from a list of common metabolite names

Output

The output would be the reaction listed in HMDB, and saved to an output file. This file can be merged with the default file included in MADRID (i.e., bcell_boundary_rxns.csv).

JoshLoecker commented 1 year ago

Started in branch https://github.com/HelikarLab/MADRID/tree/feature/issue_90

JoshLoecker commented 1 year ago

This has been reworked to include a more readable input list, such as follows

Reaction Abbreviation Compartment Minimum Reaction Rate Maximum Reaction Rate
Exchange glc_D Extracellular -100 1000
Demand 15HPETATP Cytosol -1 1000
Sink met_L Internal Membranes -1000 1