How exactly does NetPathMiner parse KGML files and distinguish between metabolic and non-metabolic pathways?

[yanshen2953]

I carefully read through the official KEGG documentation, and I could not find any explicit statement regarding the distinction between metabolic and non-metabolic pathways. Even in metabolic pathways, such as map00965, there are still signaling pathway components.

When using the KGML2igraph function and setting parse.as = "meta", the script still processes all KGML files and iterates through all reactions. However, there seems to be a specific rule that determines whether a reaction is metabolic or non-metabolic. Is this correct?

Since the corresponding logic for this is implemented in a C++ file, I am unable to read and fully understand it. I would like to know the exact logic or criteria the author used to make this distinction. This is extremely important to me. Thank you!