This addresses #285 by keeping only one instance of location-specific small molecule classes. For example, the instance ID gomodel:CHEBI_16975_cytosol (1-acyl-sn-glycerol 3-phosphate) is an output of two reactions and an input of one, which effectively combines two branches of the pathway PWY3O-6635 superpathway of phosphatidate biosynthesis.
Noting that this logic is still (for now) specific to YeastPathways with Reactome explicitly excluded. I will submit a separate, isolated PR to remove this Reactome exclusion when we're OK to do that.
This addresses #285 by keeping only one instance of location-specific small molecule classes. For example, the instance ID
gomodel:CHEBI_16975_cytosol(1-acyl-sn-glycerol 3-phosphate) is an output of two reactions and an input of one, which effectively combines two branches of the pathway PWY3O-6635 superpathway of phosphatidate biosynthesis.Noting that this logic is still (for now) specific to YeastPathways with Reactome explicitly excluded. I will submit a separate, isolated PR to remove this Reactome exclusion when we're OK to do that.