Good day all,

I have a question which I can't seem to find a specific answer for - is it possible to query KEGG via keggrest in R, and return organism specific pathways for kegg compound ids?

For example in Arabidopsis -

for genes - I can do this - linkd_data<-keggLink("pathway","ath:AT1G22430") and get

> linkd_data[[1]]
[1] "path:ath00010"

where this is arabidopsis specific pathway (or general pathways which are known to be in arabidopsis) as explained here - https://www.genome.jp/kegg/kegg3a.html

or I can do this as well - pathways.list <- keggList("pathway", "ath") to get the entire flatfile for ATH specific pathways.

So I was trying to do this for compounds - comp_data<-keggLink("pathway","cpd:C00001") For which I get back -

comp_data[[1]]
[1] "path:map00190"

the pathways returned being the reference pathways as explained in the link above.

Is there any variation of kegglink() or another function/command to specifically get arabidopsis (or any other organism) specific pathways given certain compound KEGG ids?

any help would be appreciated. Thanks!