The map file provided by franzosa is what I am looking for in a few days before. MetaCyc pathway hierarchical structure like KEGG pathway map file? . At that time, without any reply in my topic, I created such a pathway map file for the downstream analysis. The difference between this file and mine is that I only kept the superclass1 and 2 and trimmed the longer lineage for convenience in data analysis. What you need for “Carbohydrate Degradation” is in the superclass2. I followed the naming with MetaCyc website. See the R package file2meco (GitHub - ChiLiubio/file2meco: Tranform files to the microtable object in microeco package) and data/MetaCyc_pathway_map.RData in it if it is useful.
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