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).
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).